diff --git a/Examples/Makefile.in b/Examples/Makefile.in
index f85075906..9ac981f6c 100644
--- a/Examples/Makefile.in
+++ b/Examples/Makefile.in
@@ -316,6 +316,7 @@ python_clean:
 	rm -f *_wrap* *~ .~* mypython@EXEEXT@ *.pyc
 	rm -f core @EXTRA_CLEAN@
 	rm -f *.@OBJEXT@ *@SO@ *@PYTHON_SO@
+	if [ -f runme.py ]; then (rm -f runme3.py runme3.py.bak;) fi;
 
 
 ##################################################################
diff --git a/Examples/test-suite/python/Makefile.in b/Examples/test-suite/python/Makefile.in
index ec9bb7461..69ff7ca1b 100644
--- a/Examples/test-suite/python/Makefile.in
+++ b/Examples/test-suite/python/Makefile.in
@@ -112,15 +112,15 @@ VALGRIND_OPT += --suppressions=pythonswig.supp
 
 run_python = env LD_LIBRARY_PATH=.:$$LD_LIBRARY_PATH PYTHONPATH=$(srcdir):$$PYTHONPATH $(RUNTOOL) $(PYTHON) $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX)
 
+py2_runme = $(srcdir)/$(SCRIPTPREFIX)$*$(PY2SCRIPTSUFFIX)
+py3_runme = $(srcdir)/$(SCRIPTPREFIX)$*$(PY3SCRIPTSUFFIX)
+
 ifeq (,$(PY3))
 run_testcase = \
 	if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then (	  \
 	  $(run_python);)\
 	fi;
 else
-py2_runme = $(srcdir)/$(SCRIPTPREFIX)$*$(PY2SCRIPTSUFFIX)
-py3_runme = $(srcdir)/$(SCRIPTPREFIX)$*$(PY3SCRIPTSUFFIX) 
-
 run_testcase = \
 	if [ -f $(py2_runme) ]; then (	  \
 	  $(MAKE) -f $(srcdir)/Makefile $(py3_runme) && \
@@ -134,6 +134,8 @@ endif
 %.clean:
 	@rm -f hugemod.h hugemod_a.i hugemod_b.i hugemod_a.py hugemod_b.py hugemod_runme.py
 	@rm -f $*.py;
+	@#We only remove the _runme3.py if it is generated by 2to3 from a _runme.py.
+	@if [ -f $(py2_runme) ]; then (rm -f $(py3_runme) $(py3_runme).bak;) fi;
 
 clean:
 	$(MAKE) -f $(top_builddir)/$(EXAMPLES)/Makefile python_clean