diff --git a/codebase_rag/cypher_queries.py b/codebase_rag/cypher_queries.py
index 8d70bae4e..82e007bbb 100644
--- a/codebase_rag/cypher_queries.py
+++ b/codebase_rag/cypher_queries.py
@@ -52,8 +52,8 @@
 CYPHER_EXAMPLE_LIMIT_ONE = """MATCH (f:File) RETURN f.path as path, f.name as name, labels(f) as type LIMIT 1"""
 
 CYPHER_EXAMPLE_CLASS_METHODS = f"""MATCH (c:Class)-[:DEFINES_METHOD]->(m:Method)
-WHERE c.qualified_name ENDS WITH '.UserService'
-RETURN m.name AS name, m.qualified_name AS qualified_name, labels(m) AS type
+WHERE c.name = 'UserService'
+RETURN c.name AS className, m.name AS methodName, m.qualified_name AS qualified_name, labels(m) AS type
 LIMIT {CYPHER_DEFAULT_LIMIT}"""
 
 CYPHER_EXPORT_NODES = """
diff --git a/codebase_rag/prompts.py b/codebase_rag/prompts.py
index de5cce132..48bbe8d4b 100644
--- a/codebase_rag/prompts.py
+++ b/codebase_rag/prompts.py
@@ -196,6 +196,14 @@ def build_rag_orchestrator_prompt(tools: list["Tool"]) -> str:
     - CORRECT: `MATCH (c:Class) RETURN count(c) AS total`
     - WRONG: `MATCH (c:Class) RETURN c.name, count(c) AS total` (returns all items!)
 
+**VALUE PATTERN RULES (CRITICAL FOR NAME MATCHING):**
+- The `qualified_name` property contains FULL paths like: `'Project.folder.subfolder.ClassName'`
+- When users mention a class or function by SHORT NAME (e.g., "VatManager", "UserService"), you MUST match using the `name` property, NOT `qualified_name`.
+- CORRECT: `WHERE c.name = 'VatManager'`
+- WRONG: `WHERE c.qualified_name = 'VatManager'` (will never match!)
+- Use `DEFINES_METHOD` relationship to find methods of a class.
+- Use `DEFINES` relationship to find functions/classes defined in a module.
+
 **Examples:**
 
 *   **Natural Language:** "How many classes are there?"
@@ -235,7 +243,7 @@ def build_rag_orchestrator_prompt(tools: list["Tool"]) -> str:
     ```
 
 *   **Natural Language:** "What methods does UserService have?" or "Show me methods in UserService" or "List UserService methods"
-*   **Cypher Query (Use ENDS WITH to match class by short name):**
+*   **Cypher Query (Note: match by `name` property, use `DEFINES_METHOD` relationship):**
     ```cypher
     {CYPHER_EXAMPLE_CLASS_METHODS}
     ```
diff --git a/codebase_rag/services/llm.py b/codebase_rag/services/llm.py
index 018ccc1af..0ab738eae 100644
--- a/codebase_rag/services/llm.py
+++ b/codebase_rag/services/llm.py
@@ -26,9 +26,30 @@ def _create_provider_model(config: ModelConfig) -> Model:
 
 
 def _clean_cypher_response(response_text: str) -> str:
-    query = response_text.strip().replace(cs.CYPHER_BACKTICK, "")
-    if query.startswith(cs.CYPHER_PREFIX):
-        query = query[len(cs.CYPHER_PREFIX) :].strip()
+    """Clean LLM response to extract pure Cypher query.
+
+    Handles markdown formatting that models sometimes output:
+    - Triple backticks (```cypher ... ```)
+    - Bold text (**Cypher Query:**)
+    - Headers and other markdown
+    """
+    import re
+
+    query = response_text.strip()
+
+    # Extract content from code blocks if present (```cypher ... ``` or ``` ... ```)
+    code_block_match = re.search(r"```(?:cypher)?\s*(.*?)```", query, re.DOTALL | re.IGNORECASE)
+    if code_block_match:
+        query = code_block_match.group(1).strip()
+    else:
+        # Remove markdown bold/headers (e.g., **Cypher Query:**)
+        query = re.sub(r"\*\*[^*]+\*\*:?\s*", "", query)
+        # Remove single backticks
+        query = query.replace(cs.CYPHER_BACKTICK, "")
+        # Remove "cypher" prefix if present
+        if query.lower().startswith(cs.CYPHER_PREFIX):
+            query = query[len(cs.CYPHER_PREFIX):].strip()
+
     if not query.endswith(cs.CYPHER_SEMICOLON):
         query += cs.CYPHER_SEMICOLON
     return query