diff --git a/gtsam/discrete/Assignment.h b/gtsam/discrete/Assignment.h
index 90e2dbdd83..c6e426ca15 100644
--- a/gtsam/discrete/Assignment.h
+++ b/gtsam/discrete/Assignment.h
@@ -11,15 +11,17 @@
 
 /**
  * @file    Assignment.h
- * @brief    An assignment from labels to a discrete value index (size_t)
+ * @brief   An assignment from labels to a discrete value index (size_t)
  * @author  Frank Dellaert
  * @date    Feb 5, 2012
  */
 
 #pragma once
 
+#include <functional>
 #include <iostream>
 #include <map>
+#include <sstream>
 #include <utility>
 #include <vector>
 
@@ -32,13 +34,30 @@ namespace gtsam {
  */
 template <class L>
 class Assignment : public std::map<L, size_t> {
+  /**
+   * @brief Default method used by `labelFormatter` or `valueFormatter` when
+   * printing.
+   *
+   * @param x The value passed to format.
+   * @return std::string
+   */
+  static std::string DefaultFormatter(const L& x) {
+    std::stringstream ss;
+    ss << x;
+    return ss.str();
+  }
+
  public:
   using std::map<L, size_t>::operator=;
 
-  void print(const std::string& s = "Assignment: ") const {
+  void print(const std::string& s = "Assignment: ",
+             const std::function<std::string(L)>& labelFormatter =
+                 &DefaultFormatter) const {
     std::cout << s << ": ";
-    for (const typename Assignment::value_type& keyValue : *this)
-      std::cout << "(" << keyValue.first << ", " << keyValue.second << ")";
+    for (const typename Assignment::value_type& keyValue : *this) {
+      std::cout << "(" << labelFormatter(keyValue.first) << ", "
+                << keyValue.second << ")";
+    }
     std::cout << std::endl;
   }
 
diff --git a/gtsam/hybrid/GaussianMixture.cpp b/gtsam/hybrid/GaussianMixture.cpp
index 6816dfbf67..3a654ddade 100644
--- a/gtsam/hybrid/GaussianMixture.cpp
+++ b/gtsam/hybrid/GaussianMixture.cpp
@@ -119,11 +119,12 @@ void GaussianMixture::print(const std::string &s,
       "", [&](Key k) { return formatter(k); },
       [&](const GaussianConditional::shared_ptr &gf) -> std::string {
         RedirectCout rd;
-        if (gf && !gf->empty())
+        if (gf && !gf->empty()) {
           gf->print("", formatter);
-        else
-          return {"nullptr"};
-        return rd.str();
+          return rd.str();
+        } else {
+          return "nullptr";
+        }
       });
 }
 
diff --git a/gtsam/hybrid/HybridBayesNet.cpp b/gtsam/hybrid/HybridBayesNet.cpp
index bca50a902e..7889707900 100644
--- a/gtsam/hybrid/HybridBayesNet.cpp
+++ b/gtsam/hybrid/HybridBayesNet.cpp
@@ -31,8 +31,32 @@ static std::set<DiscreteKey> DiscreteKeysAsSet(const DiscreteKeys &dkeys) {
 }
 
 /* ************************************************************************* */
-HybridBayesNet HybridBayesNet::prune(
-    const DecisionTreeFactor::shared_ptr &discreteFactor) const {
+DecisionTreeFactor::shared_ptr HybridBayesNet::discreteConditionals() const {
+  AlgebraicDecisionTree<Key> decisionTree;
+
+  // The canonical decision tree factor which will get the discrete conditionals
+  // added to it.
+  DecisionTreeFactor dtFactor;
+
+  for (size_t i = 0; i < this->size(); i++) {
+    HybridConditional::shared_ptr conditional = this->at(i);
+    if (conditional->isDiscrete()) {
+      // Convert to a DecisionTreeFactor and add it to the main factor.
+      DecisionTreeFactor f(*conditional->asDiscreteConditional());
+      dtFactor = dtFactor * f;
+    }
+  }
+  return boost::make_shared<DecisionTreeFactor>(dtFactor);
+}
+
+/* ************************************************************************* */
+HybridBayesNet HybridBayesNet::prune(size_t maxNrLeaves) const {
+  // Get the decision tree of only the discrete keys
+  auto discreteConditionals = this->discreteConditionals();
+  const DecisionTreeFactor::shared_ptr discreteFactor =
+      boost::make_shared<DecisionTreeFactor>(
+          discreteConditionals->prune(maxNrLeaves));
+
   /* To Prune, we visitWith every leaf in the GaussianMixture.
    * For each leaf, using the assignment we can check the discrete decision tree
    * for 0.0 probability, then just set the leaf to a nullptr.
diff --git a/gtsam/hybrid/HybridBayesNet.h b/gtsam/hybrid/HybridBayesNet.h
index e84103a50c..b8234d70ab 100644
--- a/gtsam/hybrid/HybridBayesNet.h
+++ b/gtsam/hybrid/HybridBayesNet.h
@@ -73,6 +73,8 @@ class GTSAM_EXPORT HybridBayesNet : public BayesNet<HybridConditional> {
         HybridConditional(boost::make_shared<DiscreteConditional>(key, table)));
   }
 
+  using Base::push_back;
+
   /// Get a specific Gaussian mixture by index `i`.
   GaussianMixture::shared_ptr atMixture(size_t i) const;
 
@@ -109,9 +111,17 @@ class GTSAM_EXPORT HybridBayesNet : public BayesNet<HybridConditional> {
    */
   VectorValues optimize(const DiscreteValues &assignment) const;
 
-  /// Prune the Hybrid Bayes Net given the discrete decision tree.
-  HybridBayesNet prune(
-      const DecisionTreeFactor::shared_ptr &discreteFactor) const;
+ protected:
+  /**
+   * @brief Get all the discrete conditionals as a decision tree factor.
+   *
+   * @return DecisionTreeFactor::shared_ptr
+   */
+  DecisionTreeFactor::shared_ptr discreteConditionals() const;
+
+ public:
+  /// Prune the Hybrid Bayes Net such that we have at most maxNrLeaves leaves.
+  HybridBayesNet prune(size_t maxNrLeaves) const;
 
   /// @}
 
diff --git a/gtsam/hybrid/HybridBayesTree.cpp b/gtsam/hybrid/HybridBayesTree.cpp
index 3fa4d6268b..8fb487ae20 100644
--- a/gtsam/hybrid/HybridBayesTree.cpp
+++ b/gtsam/hybrid/HybridBayesTree.cpp
@@ -89,12 +89,12 @@ struct HybridAssignmentData {
         gaussianbayesTree_(gbt) {}
 
   /**
-   * @brief A function used during tree traversal that operators on each node
+   * @brief A function used during tree traversal that operates on each node
    * before visiting the node's children.
    *
    * @param node The current node being visited.
    * @param parentData The HybridAssignmentData from the parent node.
-   * @return HybridAssignmentData
+   * @return HybridAssignmentData which is passed to the children.
    */
   static HybridAssignmentData AssignmentPreOrderVisitor(
       const HybridBayesTree::sharedNode& node,
@@ -144,4 +144,61 @@ VectorValues HybridBayesTree::optimize(const DiscreteValues& assignment) const {
   return result;
 }
 
+/* ************************************************************************* */
+void HybridBayesTree::prune(const size_t maxNrLeaves) {
+  auto decisionTree = boost::dynamic_pointer_cast<DecisionTreeFactor>(
+      this->roots_.at(0)->conditional()->inner());
+
+  DecisionTreeFactor prunedDiscreteFactor = decisionTree->prune(maxNrLeaves);
+  decisionTree->root_ = prunedDiscreteFactor.root_;
+
+  /// Helper struct for pruning the hybrid bayes tree.
+  struct HybridPrunerData {
+    /// The discrete decision tree after pruning.
+    DecisionTreeFactor prunedDiscreteFactor;
+    HybridPrunerData(const DecisionTreeFactor& prunedDiscreteFactor,
+                     const HybridBayesTree::sharedNode& parentClique)
+        : prunedDiscreteFactor(prunedDiscreteFactor) {}
+
+    /**
+     * @brief A function used during tree traversal that operates on each node
+     * before visiting the node's children.
+     *
+     * @param node The current node being visited.
+     * @param parentData The data from the parent node.
+     * @return HybridPrunerData which is passed to the children.
+     */
+    static HybridPrunerData AssignmentPreOrderVisitor(
+        const HybridBayesTree::sharedNode& clique,
+        HybridPrunerData& parentData) {
+      // Get the conditional
+      HybridConditional::shared_ptr conditional = clique->conditional();
+
+      // If conditional is hybrid, we prune it.
+      if (conditional->isHybrid()) {
+        auto gaussianMixture = conditional->asMixture();
+
+        // Check if the number of discrete keys match,
+        // else we get an assignment error.
+        // TODO(Varun) Update prune method to handle assignment subset?
+        if (gaussianMixture->discreteKeys() ==
+            parentData.prunedDiscreteFactor.discreteKeys()) {
+          gaussianMixture->prune(parentData.prunedDiscreteFactor);
+        }
+      }
+      return parentData;
+    }
+  };
+
+  HybridPrunerData rootData(prunedDiscreteFactor, 0);
+  {
+    treeTraversal::no_op visitorPost;
+    // Limits OpenMP threads since we're mixing TBB and OpenMP
+    TbbOpenMPMixedScope threadLimiter;
+    treeTraversal::DepthFirstForestParallel(
+        *this, rootData, HybridPrunerData::AssignmentPreOrderVisitor,
+        visitorPost);
+  }
+}
+
 }  // namespace gtsam
diff --git a/gtsam/hybrid/HybridBayesTree.h b/gtsam/hybrid/HybridBayesTree.h
index 3fa344d4dd..d443e33c4c 100644
--- a/gtsam/hybrid/HybridBayesTree.h
+++ b/gtsam/hybrid/HybridBayesTree.h
@@ -88,6 +88,13 @@ class GTSAM_EXPORT HybridBayesTree : public BayesTree<HybridBayesTreeClique> {
    */
   VectorValues optimize(const DiscreteValues& assignment) const;
 
+  /**
+   * @brief Prune the underlying Bayes tree.
+   *
+   * @param maxNumberLeaves The max number of leaf nodes to keep.
+   */
+  void prune(const size_t maxNumberLeaves);
+
   /// @}
 
  private:
diff --git a/gtsam/hybrid/HybridConditional.h b/gtsam/hybrid/HybridConditional.h
index b43bb9945d..93ce33bea1 100644
--- a/gtsam/hybrid/HybridConditional.h
+++ b/gtsam/hybrid/HybridConditional.h
@@ -34,8 +34,6 @@
 
 namespace gtsam {
 
-class HybridGaussianFactorGraph;
-
 /**
  * Hybrid Conditional Density
  *
diff --git a/gtsam/hybrid/HybridFactorGraph.h b/gtsam/hybrid/HybridFactorGraph.h
index fc730f0c97..05a17b000f 100644
--- a/gtsam/hybrid/HybridFactorGraph.h
+++ b/gtsam/hybrid/HybridFactorGraph.h
@@ -135,6 +135,28 @@ class HybridFactorGraph : public FactorGraph<HybridFactor> {
       push_hybrid(p);
     }
   }
+
+  /// Get all the discrete keys in the factor graph.
+  const KeySet discreteKeys() const {
+    KeySet discrete_keys;
+    for (auto& factor : factors_) {
+      for (const DiscreteKey& k : factor->discreteKeys()) {
+        discrete_keys.insert(k.first);
+      }
+    }
+    return discrete_keys;
+  }
+
+  /// Get all the continuous keys in the factor graph.
+  const KeySet continuousKeys() const {
+    KeySet keys;
+    for (auto& factor : factors_) {
+      for (const Key& key : factor->continuousKeys()) {
+        keys.insert(key);
+      }
+    }
+    return keys;
+  }
 };
 
 }  // namespace gtsam
diff --git a/gtsam/hybrid/HybridGaussianFactorGraph.cpp b/gtsam/hybrid/HybridGaussianFactorGraph.cpp
index 09b592bd69..0faf0e86e4 100644
--- a/gtsam/hybrid/HybridGaussianFactorGraph.cpp
+++ b/gtsam/hybrid/HybridGaussianFactorGraph.cpp
@@ -96,8 +96,12 @@ GaussianMixtureFactor::Sum sumFrontals(
       }
 
     } else if (f->isContinuous()) {
-      deferredFactors.push_back(
-          boost::dynamic_pointer_cast<HybridGaussianFactor>(f)->inner());
+      if (auto gf = boost::dynamic_pointer_cast<HybridGaussianFactor>(f)) {
+        deferredFactors.push_back(gf->inner());
+      }
+      if (auto cg = boost::dynamic_pointer_cast<HybridConditional>(f)) {
+        deferredFactors.push_back(cg->asGaussian());
+      }
 
     } else if (f->isDiscrete()) {
       // Don't do anything for discrete-only factors
@@ -404,31 +408,9 @@ void HybridGaussianFactorGraph::add(DecisionTreeFactor::shared_ptr factor) {
   FactorGraph::add(boost::make_shared<HybridDiscreteFactor>(factor));
 }
 
-/* ************************************************************************ */
-const KeySet HybridGaussianFactorGraph::getDiscreteKeys() const {
-  KeySet discrete_keys;
-  for (auto &factor : factors_) {
-    for (const DiscreteKey &k : factor->discreteKeys()) {
-      discrete_keys.insert(k.first);
-    }
-  }
-  return discrete_keys;
-}
-
-/* ************************************************************************ */
-const KeySet HybridGaussianFactorGraph::getContinuousKeys() const {
-  KeySet keys;
-  for (auto &factor : factors_) {
-    for (const Key &key : factor->continuousKeys()) {
-      keys.insert(key);
-    }
-  }
-  return keys;
-}
-
 /* ************************************************************************ */
 const Ordering HybridGaussianFactorGraph::getHybridOrdering() const {
-  KeySet discrete_keys = getDiscreteKeys();
+  KeySet discrete_keys = discreteKeys();
   for (auto &factor : factors_) {
     for (const DiscreteKey &k : factor->discreteKeys()) {
       discrete_keys.insert(k.first);
diff --git a/gtsam/hybrid/HybridGaussianFactorGraph.h b/gtsam/hybrid/HybridGaussianFactorGraph.h
index ad5cde09b0..bd24cdeaa7 100644
--- a/gtsam/hybrid/HybridGaussianFactorGraph.h
+++ b/gtsam/hybrid/HybridGaussianFactorGraph.h
@@ -161,12 +161,6 @@ class GTSAM_EXPORT HybridGaussianFactorGraph
     }
   }
 
-  /// Get all the discrete keys in the factor graph.
-  const KeySet getDiscreteKeys() const;
-
-  /// Get all the continuous keys in the factor graph.
-  const KeySet getContinuousKeys() const;
-
   /**
    * @brief Return a Colamd constrained ordering where the discrete keys are
    * eliminated after the continuous keys.
diff --git a/gtsam/hybrid/HybridGaussianISAM.cpp b/gtsam/hybrid/HybridGaussianISAM.cpp
index 23a95c021d..57e50104d7 100644
--- a/gtsam/hybrid/HybridGaussianISAM.cpp
+++ b/gtsam/hybrid/HybridGaussianISAM.cpp
@@ -14,9 +14,10 @@
  * @date March 31, 2022
  * @author Fan Jiang
  * @author Frank Dellaert
- * @author Richard Roberts
+ * @author Varun Agrawal
  */
 
+#include <gtsam/base/treeTraversal-inst.h>
 #include <gtsam/hybrid/HybridBayesTree.h>
 #include <gtsam/hybrid/HybridGaussianFactorGraph.h>
 #include <gtsam/hybrid/HybridGaussianISAM.h>
@@ -41,6 +42,7 @@ HybridGaussianISAM::HybridGaussianISAM(const HybridBayesTree& bayesTree)
 void HybridGaussianISAM::updateInternal(
     const HybridGaussianFactorGraph& newFactors,
     HybridBayesTree::Cliques* orphans,
+    const boost::optional<size_t>& maxNrLeaves,
     const boost::optional<Ordering>& ordering,
     const HybridBayesTree::Eliminate& function) {
   // Remove the contaminated part of the Bayes tree
@@ -60,23 +62,24 @@ void HybridGaussianISAM::updateInternal(
   for (const sharedClique& orphan : *orphans)
     factors += boost::make_shared<BayesTreeOrphanWrapper<Node> >(orphan);
 
-  KeySet allDiscrete;
-  for (auto& factor : factors) {
-    for (auto& k : factor->discreteKeys()) {
-      allDiscrete.insert(k.first);
-    }
-  }
+  // Get all the discrete keys from the factors
+  KeySet allDiscrete = factors.discreteKeys();
+
+  // Create KeyVector with continuous keys followed by discrete keys.
   KeyVector newKeysDiscreteLast;
+  // Insert continuous keys first.
   for (auto& k : newFactorKeys) {
     if (!allDiscrete.exists(k)) {
       newKeysDiscreteLast.push_back(k);
     }
   }
+  // Insert discrete keys at the end
   std::copy(allDiscrete.begin(), allDiscrete.end(),
             std::back_inserter(newKeysDiscreteLast));
 
   // Get an ordering where the new keys are eliminated last
   const VariableIndex index(factors);
+
   Ordering elimination_ordering;
   if (ordering) {
     elimination_ordering = *ordering;
@@ -91,6 +94,10 @@ void HybridGaussianISAM::updateInternal(
   HybridBayesTree::shared_ptr bayesTree =
       factors.eliminateMultifrontal(elimination_ordering, function, index);
 
+  if (maxNrLeaves) {
+    bayesTree->prune(*maxNrLeaves);
+  }
+
   // Re-add into Bayes tree data structures
   this->roots_.insert(this->roots_.end(), bayesTree->roots().begin(),
                       bayesTree->roots().end());
@@ -99,61 +106,11 @@ void HybridGaussianISAM::updateInternal(
 
 /* ************************************************************************* */
 void HybridGaussianISAM::update(const HybridGaussianFactorGraph& newFactors,
+                                const boost::optional<size_t>& maxNrLeaves,
                                 const boost::optional<Ordering>& ordering,
                                 const HybridBayesTree::Eliminate& function) {
   Cliques orphans;
-  this->updateInternal(newFactors, &orphans, ordering, function);
-}
-
-/* ************************************************************************* */
-/**
- * @brief Check if `b` is a subset of `a`.
- * Non-const since they need to be sorted.
- *
- * @param a KeyVector
- * @param b KeyVector
- * @return True if the keys of b is a subset of a, else false.
- */
-bool IsSubset(KeyVector a, KeyVector b) {
-  std::sort(a.begin(), a.end());
-  std::sort(b.begin(), b.end());
-  return std::includes(a.begin(), a.end(), b.begin(), b.end());
-}
-
-/* ************************************************************************* */
-void HybridGaussianISAM::prune(const Key& root, const size_t maxNrLeaves) {
-  auto decisionTree = boost::dynamic_pointer_cast<DecisionTreeFactor>(
-      this->clique(root)->conditional()->inner());
-  DecisionTreeFactor prunedDiscreteFactor = decisionTree->prune(maxNrLeaves);
-  decisionTree->root_ = prunedDiscreteFactor.root_;
-
-  std::vector<gtsam::Key> prunedKeys;
-  for (auto&& clique : nodes()) {
-    // The cliques can be repeated for each frontal so we record it in
-    // prunedKeys and check if we have already pruned a particular clique.
-    if (std::find(prunedKeys.begin(), prunedKeys.end(), clique.first) !=
-        prunedKeys.end()) {
-      continue;
-    }
-
-    // Add all the keys of the current clique to be pruned to prunedKeys
-    for (auto&& key : clique.second->conditional()->frontals()) {
-      prunedKeys.push_back(key);
-    }
-
-    // Convert parents() to a KeyVector for comparison
-    KeyVector parents;
-    for (auto&& parent : clique.second->conditional()->parents()) {
-      parents.push_back(parent);
-    }
-
-    if (IsSubset(parents, decisionTree->keys())) {
-      auto gaussianMixture = boost::dynamic_pointer_cast<GaussianMixture>(
-          clique.second->conditional()->inner());
-
-      gaussianMixture->prune(prunedDiscreteFactor);
-    }
-  }
+  this->updateInternal(newFactors, &orphans, maxNrLeaves, ordering, function);
 }
 
 }  // namespace gtsam
diff --git a/gtsam/hybrid/HybridGaussianISAM.h b/gtsam/hybrid/HybridGaussianISAM.h
index ff09787293..a6a82b3e89 100644
--- a/gtsam/hybrid/HybridGaussianISAM.h
+++ b/gtsam/hybrid/HybridGaussianISAM.h
@@ -48,6 +48,7 @@ class GTSAM_EXPORT HybridGaussianISAM : public ISAM<HybridBayesTree> {
   void updateInternal(
       const HybridGaussianFactorGraph& newFactors,
       HybridBayesTree::Cliques* orphans,
+      const boost::optional<size_t>& maxNrLeaves = boost::none,
       const boost::optional<Ordering>& ordering = boost::none,
       const HybridBayesTree::Eliminate& function =
           HybridBayesTree::EliminationTraitsType::DefaultEliminate);
@@ -57,20 +58,15 @@ class GTSAM_EXPORT HybridGaussianISAM : public ISAM<HybridBayesTree> {
    * @brief Perform update step with new factors.
    *
    * @param newFactors Factor graph of new factors to add and eliminate.
+   * @param maxNrLeaves The maximum number of leaves to keep after pruning.
+   * @param ordering Custom elimination ordering.
    * @param function Elimination function.
    */
   void update(const HybridGaussianFactorGraph& newFactors,
+              const boost::optional<size_t>& maxNrLeaves = boost::none,
               const boost::optional<Ordering>& ordering = boost::none,
               const HybridBayesTree::Eliminate& function =
                   HybridBayesTree::EliminationTraitsType::DefaultEliminate);
-
-  /**
-   * @brief Prune the underlying Bayes tree.
-   * 
-   * @param root The root key in the discrete conditional decision tree.
-   * @param maxNumberLeaves 
-   */
-  void prune(const Key& root, const size_t maxNumberLeaves);
 };
 
 /// traits
diff --git a/gtsam/hybrid/HybridNonlinearISAM.cpp b/gtsam/hybrid/HybridNonlinearISAM.cpp
index 36cda4e807..d05e081dd4 100644
--- a/gtsam/hybrid/HybridNonlinearISAM.cpp
+++ b/gtsam/hybrid/HybridNonlinearISAM.cpp
@@ -33,7 +33,9 @@ void HybridNonlinearISAM::saveGraph(const string& s,
 
 /* ************************************************************************* */
 void HybridNonlinearISAM::update(const HybridNonlinearFactorGraph& newFactors,
-                                 const Values& initialValues) {
+                                 const Values& initialValues,
+                                 const boost::optional<size_t>& maxNrLeaves,
+                                 const boost::optional<Ordering>& ordering) {
   if (newFactors.size() > 0) {
     // Reorder and relinearize every reorderInterval updates
     if (reorderInterval_ > 0 && ++reorderCounter_ >= reorderInterval_) {
@@ -51,7 +53,8 @@ void HybridNonlinearISAM::update(const HybridNonlinearFactorGraph& newFactors,
         newFactors.linearize(linPoint_);
 
     // Update ISAM
-    isam_.update(*linearizedNewFactors, boost::none, eliminationFunction_);
+    isam_.update(*linearizedNewFactors, maxNrLeaves, ordering,
+                 eliminationFunction_);
   }
 }
 
@@ -66,7 +69,7 @@ void HybridNonlinearISAM::reorder_relinearize() {
     // Just recreate the whole BayesTree
     // TODO: allow for constrained ordering here
     // TODO: decouple relinearization and reordering to avoid
-    isam_.update(*factors_.linearize(newLinPoint), boost::none,
+    isam_.update(*factors_.linearize(newLinPoint), boost::none, boost::none,
                  eliminationFunction_);
 
     // Update linearization point
diff --git a/gtsam/hybrid/HybridNonlinearISAM.h b/gtsam/hybrid/HybridNonlinearISAM.h
index d96485fff0..47aa81c558 100644
--- a/gtsam/hybrid/HybridNonlinearISAM.h
+++ b/gtsam/hybrid/HybridNonlinearISAM.h
@@ -82,12 +82,9 @@ class GTSAM_EXPORT HybridNonlinearISAM {
   /**
    * @brief Prune the underlying Bayes tree.
    *
-   * @param root The root key in the discrete conditional decision tree.
-   * @param maxNumberLeaves
+   * @param maxNumberLeaves The max number of leaf nodes to keep.
    */
-  void prune(const Key& root, const size_t maxNumberLeaves) {
-    isam_.prune(root, maxNumberLeaves);
-  }
+  void prune(const size_t maxNumberLeaves) { isam_.prune(maxNumberLeaves); }
 
   /** Return the current linearization point */
   const Values& getLinearizationPoint() const { return linPoint_; }
@@ -121,7 +118,9 @@ class GTSAM_EXPORT HybridNonlinearISAM {
 
   /** Add new factors along with their initial linearization points */
   void update(const HybridNonlinearFactorGraph& newFactors,
-              const Values& initialValues);
+              const Values& initialValues,
+              const boost::optional<size_t>& maxNrLeaves = boost::none,
+              const boost::optional<Ordering>& ordering = boost::none);
 
   /** Relinearization and reordering of variables */
   void reorder_relinearize();
diff --git a/gtsam/hybrid/tests/Switching.h b/gtsam/hybrid/tests/Switching.h
index 8bcb26c927..3ae8f0bb1c 100644
--- a/gtsam/hybrid/tests/Switching.h
+++ b/gtsam/hybrid/tests/Switching.h
@@ -115,7 +115,6 @@ inline std::pair<KeyVector, std::vector<int>> makeBinaryOrdering(
 /* ***************************************************************************
  */
 using MotionModel = BetweenFactor<double>;
-// using MotionMixture = MixtureFactor<MotionModel>;
 
 // Test fixture with switching network.
 struct Switching {
@@ -125,7 +124,13 @@ struct Switching {
   HybridGaussianFactorGraph linearizedFactorGraph;
   Values linearizationPoint;
 
-  /// Create with given number of time steps.
+  /**
+   * @brief Create with given number of time steps.
+   *
+   * @param K The total number of timesteps.
+   * @param between_sigma The stddev between poses.
+   * @param prior_sigma The stddev on priors (also used for measurements).
+   */
   Switching(size_t K, double between_sigma = 1.0, double prior_sigma = 0.1)
       : K(K) {
     // Create DiscreteKeys for binary K modes, modes[0] will not be used.
@@ -166,6 +171,8 @@ struct Switching {
       linearizationPoint.insert<double>(X(k), static_cast<double>(k));
     }
 
+    // The ground truth is robot moving forward
+    // and one less than the linearization point
     linearizedFactorGraph = *nonlinearFactorGraph.linearize(linearizationPoint);
   }
 
diff --git a/gtsam/hybrid/tests/testHybridBayesNet.cpp b/gtsam/hybrid/tests/testHybridBayesNet.cpp
index 0c15ee83da..5885fdcdcc 100644
--- a/gtsam/hybrid/tests/testHybridBayesNet.cpp
+++ b/gtsam/hybrid/tests/testHybridBayesNet.cpp
@@ -52,6 +52,20 @@ TEST(HybridBayesNet, Creation) {
   EXPECT(df.equals(expected));
 }
 
+/* ****************************************************************************/
+// Test adding a bayes net to another one.
+TEST(HybridBayesNet, Add) {
+  HybridBayesNet bayesNet;
+
+  bayesNet.add(Asia, "99/1");
+
+  DiscreteConditional expected(Asia, "99/1");
+
+  HybridBayesNet other;
+  other.push_back(bayesNet);
+  EXPECT(bayesNet.equals(other));
+}
+
 /* ****************************************************************************/
 // Test choosing an assignment of conditionals
 TEST(HybridBayesNet, Choose) {
@@ -169,6 +183,24 @@ TEST(HybridBayesNet, OptimizeMultifrontal) {
   EXPECT(assert_equal(expectedValues, delta.continuous(), 1e-5));
 }
 
+/* ****************************************************************************/
+// Test bayes net pruning
+TEST(HybridBayesNet, Prune) {
+  Switching s(4);
+
+  Ordering hybridOrdering = s.linearizedFactorGraph.getHybridOrdering();
+  HybridBayesNet::shared_ptr hybridBayesNet =
+      s.linearizedFactorGraph.eliminateSequential(hybridOrdering);
+
+  HybridValues delta = hybridBayesNet->optimize();
+
+  auto prunedBayesNet = hybridBayesNet->prune(2);
+  HybridValues pruned_delta = prunedBayesNet.optimize();
+
+  EXPECT(assert_equal(delta.discrete(), pruned_delta.discrete()));
+  EXPECT(assert_equal(delta.continuous(), pruned_delta.continuous()));
+}
+
 /* ****************************************************************************/
 // Test HybridBayesNet serialization.
 TEST(HybridBayesNet, Serialization) {
diff --git a/gtsam/hybrid/tests/testGaussianHybridFactorGraph.cpp b/gtsam/hybrid/tests/testHybridGaussianFactorGraph.cpp
similarity index 92%
rename from gtsam/hybrid/tests/testGaussianHybridFactorGraph.cpp
rename to gtsam/hybrid/tests/testHybridGaussianFactorGraph.cpp
index 40da42412d..d199d76113 100644
--- a/gtsam/hybrid/tests/testGaussianHybridFactorGraph.cpp
+++ b/gtsam/hybrid/tests/testHybridGaussianFactorGraph.cpp
@@ -500,6 +500,7 @@ TEST(HybridGaussianFactorGraph, SwitchingTwoVar) {
   }
 }
 
+/* ************************************************************************* */
 TEST(HybridGaussianFactorGraph, optimize) {
   HybridGaussianFactorGraph hfg;
 
@@ -521,6 +522,46 @@ TEST(HybridGaussianFactorGraph, optimize) {
 
   EXPECT(assert_equal(hv.atDiscrete(C(1)), int(0)));
 }
+
+/* ************************************************************************* */
+// Test adding of gaussian conditional and re-elimination.
+TEST(HybridGaussianFactorGraph, Conditionals) {
+  Switching switching(4);
+  HybridGaussianFactorGraph hfg;
+
+  hfg.push_back(switching.linearizedFactorGraph.at(0));  // P(X1)
+  Ordering ordering;
+  ordering.push_back(X(1));
+  HybridBayesNet::shared_ptr bayes_net = hfg.eliminateSequential(ordering);
+
+  hfg.push_back(switching.linearizedFactorGraph.at(1));  // P(X1, X2 | M1)
+  hfg.push_back(*bayes_net);
+  hfg.push_back(switching.linearizedFactorGraph.at(2));  // P(X2, X3 | M2)
+  hfg.push_back(switching.linearizedFactorGraph.at(5));  // P(M1)
+  ordering.push_back(X(2));
+  ordering.push_back(X(3));
+  ordering.push_back(M(1));
+  ordering.push_back(M(2));
+
+  bayes_net = hfg.eliminateSequential(ordering);
+
+  HybridValues result = bayes_net->optimize();
+
+  Values expected_continuous;
+  expected_continuous.insert<double>(X(1), 0);
+  expected_continuous.insert<double>(X(2), 1);
+  expected_continuous.insert<double>(X(3), 2);
+  expected_continuous.insert<double>(X(4), 4);
+  Values result_continuous =
+      switching.linearizationPoint.retract(result.continuous());
+  EXPECT(assert_equal(expected_continuous, result_continuous));
+
+  DiscreteValues expected_discrete;
+  expected_discrete[M(1)] = 1;
+  expected_discrete[M(2)] = 1;
+  EXPECT(assert_equal(expected_discrete, result.discrete()));
+}
+
 /* ************************************************************************* */
 int main() {
   TestResult tr;
diff --git a/gtsam/hybrid/tests/testHybridIncremental.cpp b/gtsam/hybrid/tests/testHybridGaussianISAM.cpp
similarity index 99%
rename from gtsam/hybrid/tests/testHybridIncremental.cpp
rename to gtsam/hybrid/tests/testHybridGaussianISAM.cpp
index 8e16d02b93..a0a87933f4 100644
--- a/gtsam/hybrid/tests/testHybridIncremental.cpp
+++ b/gtsam/hybrid/tests/testHybridGaussianISAM.cpp
@@ -235,7 +235,7 @@ TEST(HybridGaussianElimination, Approx_inference) {
   size_t maxNrLeaves = 5;
   incrementalHybrid.update(graph1);
 
-  incrementalHybrid.prune(M(3), maxNrLeaves);
+  incrementalHybrid.prune(maxNrLeaves);
 
   /*
   unpruned factor is:
@@ -329,7 +329,7 @@ TEST(HybridGaussianElimination, Incremental_approximate) {
   // Run update with pruning
   size_t maxComponents = 5;
   incrementalHybrid.update(graph1);
-  incrementalHybrid.prune(M(3), maxComponents);
+  incrementalHybrid.prune(maxComponents);
 
   // Check if we have a bayes tree with 4 hybrid nodes,
   // each with 2, 4, 8, and 5 (pruned) leaves respetively.
@@ -350,7 +350,7 @@ TEST(HybridGaussianElimination, Incremental_approximate) {
 
   // Run update with pruning a second time.
   incrementalHybrid.update(graph2);
-  incrementalHybrid.prune(M(4), maxComponents);
+  incrementalHybrid.prune(maxComponents);
 
   // Check if we have a bayes tree with pruned hybrid nodes,
   // with 5 (pruned) leaves.
@@ -496,7 +496,7 @@ TEST(HybridGaussianISAM, NonTrivial) {
   // The MHS at this point should be a 2 level tree on (1, 2).
   // 1 has 2 choices, and 2 has 4 choices.
   inc.update(gfg);
-  inc.prune(M(2), 2);
+  inc.prune(2);
 
   /*************** Run Round 4 ***************/
   // Add odometry factor with discrete modes.
@@ -531,7 +531,7 @@ TEST(HybridGaussianISAM, NonTrivial) {
 
   // Keep pruning!
   inc.update(gfg);
-  inc.prune(M(3), 3);
+  inc.prune(3);
 
   // The final discrete graph should not be empty since we have eliminated
   // all continuous variables.
diff --git a/gtsam/hybrid/tests/testHybridNonlinearISAM.cpp b/gtsam/hybrid/tests/testHybridNonlinearISAM.cpp
index 46076b3306..4e1710c424 100644
--- a/gtsam/hybrid/tests/testHybridNonlinearISAM.cpp
+++ b/gtsam/hybrid/tests/testHybridNonlinearISAM.cpp
@@ -256,7 +256,7 @@ TEST(HybridNonlinearISAM, Approx_inference) {
   incrementalHybrid.update(graph1, initial);
   HybridGaussianISAM bayesTree = incrementalHybrid.bayesTree();
 
-  bayesTree.prune(M(3), maxNrLeaves);
+  bayesTree.prune(maxNrLeaves);
 
   /*
   unpruned factor is:
@@ -355,7 +355,7 @@ TEST(HybridNonlinearISAM, Incremental_approximate) {
   incrementalHybrid.update(graph1, initial);
   HybridGaussianISAM bayesTree = incrementalHybrid.bayesTree();
 
-  bayesTree.prune(M(3), maxComponents);
+  bayesTree.prune(maxComponents);
 
   // Check if we have a bayes tree with 4 hybrid nodes,
   // each with 2, 4, 8, and 5 (pruned) leaves respetively.
@@ -380,7 +380,7 @@ TEST(HybridNonlinearISAM, Incremental_approximate) {
   incrementalHybrid.update(graph2, initial);
   bayesTree = incrementalHybrid.bayesTree();
 
-  bayesTree.prune(M(4), maxComponents);
+  bayesTree.prune(maxComponents);
 
   // Check if we have a bayes tree with pruned hybrid nodes,
   // with 5 (pruned) leaves.
@@ -482,8 +482,7 @@ TEST(HybridNonlinearISAM, NonTrivial) {
   still = boost::make_shared<PlanarMotionModel>(W(1), W(2), Pose2(0, 0, 0),
                                                 noise_model);
   moving =
-      boost::make_shared<PlanarMotionModel>(W(1), W(2), odometry,
-      noise_model);
+      boost::make_shared<PlanarMotionModel>(W(1), W(2), odometry, noise_model);
   components = {moving, still};
   mixtureFactor = boost::make_shared<MixtureFactor>(
       contKeys, DiscreteKeys{gtsam::DiscreteKey(M(2), 2)}, components);
@@ -515,7 +514,7 @@ TEST(HybridNonlinearISAM, NonTrivial) {
   // The MHS at this point should be a 2 level tree on (1, 2).
   // 1 has 2 choices, and 2 has 4 choices.
   inc.update(fg, initial);
-  inc.prune(M(2), 2);
+  inc.prune(2);
 
   fg = HybridNonlinearFactorGraph();
   initial = Values();
@@ -526,8 +525,7 @@ TEST(HybridNonlinearISAM, NonTrivial) {
   still = boost::make_shared<PlanarMotionModel>(W(2), W(3), Pose2(0, 0, 0),
                                                 noise_model);
   moving =
-      boost::make_shared<PlanarMotionModel>(W(2), W(3), odometry,
-      noise_model);
+      boost::make_shared<PlanarMotionModel>(W(2), W(3), odometry, noise_model);
   components = {moving, still};
   mixtureFactor = boost::make_shared<MixtureFactor>(
       contKeys, DiscreteKeys{gtsam::DiscreteKey(M(3), 2)}, components);
@@ -551,7 +549,7 @@ TEST(HybridNonlinearISAM, NonTrivial) {
 
   // Keep pruning!
   inc.update(fg, initial);
-  inc.prune(M(3), 3);
+  inc.prune(3);
 
   fg = HybridNonlinearFactorGraph();
   initial = Values();
@@ -560,8 +558,7 @@ TEST(HybridNonlinearISAM, NonTrivial) {
 
   // The final discrete graph should not be empty since we have eliminated
   // all continuous variables.
-  auto discreteTree =
-  bayesTree[M(3)]->conditional()->asDiscreteConditional();
+  auto discreteTree = bayesTree[M(3)]->conditional()->asDiscreteConditional();
   EXPECT_LONGS_EQUAL(3, discreteTree->size());
 
   // Test if the optimal discrete mode assignment is (1, 1, 1).
diff --git a/gtsam/inference/BayesTree.h b/gtsam/inference/BayesTree.h
index 924a505a2d..b4b07a3573 100644
--- a/gtsam/inference/BayesTree.h
+++ b/gtsam/inference/BayesTree.h
@@ -33,7 +33,6 @@ namespace gtsam {
   // Forward declarations
   template<class FACTOR> class FactorGraph;
   template<class BAYESTREE, class GRAPH> class EliminatableClusterTree;
-  class HybridBayesTreeClique;
 
   /* ************************************************************************* */
   /** clique statistics */