diff --git a/Makefile b/Makefile
index aedf595aef61d102833705ad2797cc5a658da4ef..804e1c3c3c2348d98a48e8461072af5f44cfbe8f 100644
--- a/Makefile
+++ b/Makefile
@@ -275,6 +275,7 @@ TOPICS_DIR = $(PX4_BASE)src/modules/uORB/topics
 MULTIPLATFORM_HEADER_DIR = $(PX4_BASE)src/platforms/nuttx/px4_messages
 MULTIPLATFORM_PREFIX = px4_
 TOPICHEADER_TEMP_DIR = $(BUILD_DIR)topics_temporary
+MULTI_TOPICHEADER_TEMP_DIR = $(BUILD_DIR)multi_topics_temporary
 GENMSG_PYTHONPATH = $(PX4_BASE)Tools/genmsg/src
 GENCPP_PYTHONPATH = $(PX4_BASE)Tools/gencpp/src
 
@@ -287,9 +288,7 @@ generateuorbtopicheaders: checksubmodules
 	@$(ECHO) "Generating multiplatform uORB topic wrapper headers"
 	$(Q) (PYTHONPATH=$(GENMSG_PYTHONPATH):$(GENCPP_PYTHONPATH):$(PYTHONPATH) $(PYTHON) \
 		$(PX4_BASE)Tools/px_generate_uorb_topic_headers.py \
-		-d $(MSG_DIR) -o $(MULTIPLATFORM_HEADER_DIR) -e $(MULTIPLATFORM_TEMPLATE_DIR) -t $(TOPICHEADER_TEMP_DIR) -p $(MULTIPLATFORM_PREFIX))
-# clean up temporary files
-	$(Q) (rm -r $(TOPICHEADER_TEMP_DIR))
+		-d $(MSG_DIR) -o $(MULTIPLATFORM_HEADER_DIR) -e $(MULTIPLATFORM_TEMPLATE_DIR) -t $(MULTI_TOPICHEADER_TEMP_DIR) -p $(MULTIPLATFORM_PREFIX))
 
 #
 # Testing targets
@@ -320,6 +319,8 @@ clean:
 	$(Q) $(RMDIR) $(BUILD_DIR)*.build
 	$(Q) $(RMDIR) $(PX4_VERSIONING_DIR)
 	$(Q) $(REMOVE) $(IMAGE_DIR)*.px4
+	$(Q) $(RMDIR) $(TOPICHEADER_TEMP_DIR)
+	$(Q) $(RMDIR) $(MULTI_TOPICHEADER_TEMP_DIR)
 
 .PHONY:	distclean
 distclean: clean