diff --git a/Makefile b/Makefile
index 31ec128..204eae4 100644
--- a/Makefile
+++ b/Makefile
@@ -12,7 +12,7 @@ generate_ir:
 	@python3 scripts/src2ir.py
 
 clean_ir:
-	@rm examples/ir/*.ll
+	@rm examples/ir/*/*.ll
 
 clean_and_generate_ir: clean_ir generate_ir
 
diff --git a/scripts/src2ir.py b/scripts/src2ir.py
index 160e7a3..b04f5b7 100644
--- a/scripts/src2ir.py
+++ b/scripts/src2ir.py
@@ -1,36 +1,34 @@
 import os
 import subprocess
 
-def convert_cpp_to_ir(source_folder, ir_folder):
-    for file in os.listdir(source_folder):
-        if file.endswith('.cpp'):
+def convert_src_to_ir(source_folder, ir_folder):
+    # walk through all subdirectories and the corresponding source files
+    for root, _, files in os.walk(source_folder):
+        for file in files:
+            # get relative path from `source_folder` to maintain structure
+            rel_path = os.path.relpath(root, source_folder)
             base_name = os.path.splitext(file)[0]
-            source_path = os.path.join(source_folder, file)
-            ir_path = os.path.join(ir_folder, f"{base_name}_cpp.ll")
-            if not os.path.exists(ir_path):
-                # note for the clang++ command:
-                #   -O0: disable optimizations
-                #   -S: output assembly (llvm ir in this case)
-                #   -emit-llvm: generate llvm ir instead of native assembly
-                command = f"clang++ -O0 -S -emit-llvm {source_path} -o {ir_path}"
-                subprocess.run(command, shell=True, check=True)
-                print(f"converted {file} to {ir_path}")
+            
+            # create corresponding ir folder structure
+            ir_subfolder = os.path.join(ir_folder, rel_path)
+            if not os.path.exists(ir_subfolder):
+                os.makedirs(ir_subfolder)
+            
+            source_path = os.path.join(root, file)
+            if file.endswith('.cpp'):
+                ir_path = os.path.join(ir_subfolder, f"{base_name}_cpp.ll")
+            elif file.endswith('.rs'):
+                ir_path = os.path.join(ir_subfolder, f"{base_name}_rs.ll")
             else:
-                print(f"ir file {ir_path} already exists, skipping conversion.")
-
-def convert_rs_to_ir(source_folder, ir_folder):
-    for file in os.listdir(source_folder):
-        if file.endswith('.rs'):
-            base_name = os.path.splitext(file)[0]
-            source_path = os.path.join(source_folder, file)
-            ir_path = os.path.join(ir_folder, f"{base_name}_rs.ll")
+                assert False, f"unsupported file type: {file}"
+            
             if not os.path.exists(ir_path):
-                # note for the rustc command:
-                #   --emit=llvm-ir: output llvm ir
-                #   --crate-type=lib: compile as a library
-                command = f"rustc --emit=llvm-ir --crate-type=lib {source_path} -o {ir_path}"
+                if file.endswith('.cpp'):
+                    command = f"clang++ -O0 -S -emit-llvm {source_path} -o {ir_path}"
+                elif file.endswith('.rs'):
+                    command = f"rustc --emit=llvm-ir --crate-type=lib {source_path} -o {ir_path}"
                 subprocess.run(command, shell=True, check=True)
-                print(f"converted {file} to {ir_path}")
+                print(f"converted {source_path} to {ir_path}")
             else:
                 print(f"ir file {ir_path} already exists, skipping conversion.")
 
@@ -41,8 +39,7 @@ def main():
     if not os.path.exists(ir_folder):
         os.makedirs(ir_folder)
 
-    convert_cpp_to_ir(source_folder, ir_folder)
-    convert_rs_to_ir(source_folder, ir_folder)
+    convert_src_to_ir(source_folder, ir_folder)
 
 if __name__ == "__main__":
     main()
diff --git a/src/Preprocessor.h b/src/Preprocessor.h
index 085bdcb..6aa3c89 100644
--- a/src/Preprocessor.h
+++ b/src/Preprocessor.h
@@ -29,8 +29,8 @@ class Preprocessor {
             exit(1);
         }
 
-        cpp_path_ = DEFAULT_IR_DIR + base_name_ + CPP_IR_SUFFIX;
-        rust_path_ = DEFAULT_IR_DIR + base_name_ + RUST_IR_SUFFIX;
+        cpp_path_ = DEFAULT_IR_DIR + base_name_ + "/" + base_name_ + CPP_IR_SUFFIX;
+        rust_path_ = DEFAULT_IR_DIR + base_name_ + "/" + base_name_ + RUST_IR_SUFFIX;
 
         argv.push_back(&cpp_path_[0]);
         argv.push_back(&rust_path_[0]);