diff --git a/Makefile.am b/Makefile.am
index 441b226..d1ee67f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -57,7 +57,7 @@ uninstall-local: $(DOXYGEN_UNINSTALL_DATA_TARGETS)
 
 # Files to be removed in build directory
 clean-local:
-	rm -rf $(builddir)/.DS_Store
+	rm -rf $(top_builddir)/.DS_Store
 
 #
 # Additional rules
diff --git a/cscripts/Makefile.am b/cscripts/Makefile.am
index 683dc09..e13bc4e 100644
--- a/cscripts/Makefile.am
+++ b/cscripts/Makefile.am
@@ -20,7 +20,7 @@
 #############################################################################
 
 # Scripts to be distributed in $(pyexecdir)/cscripts
-pythonscripts = $(builddir)/__init__.py \
+pythonscripts = $(top_builddir)/cscripts/__init__.py \
                 $(srcdir)/cscaldb.py \
                 $(srcdir)/csinfo.py \
                 $(srcdir)/cslightcrv.py \
@@ -242,15 +242,15 @@ uninstall-hook:
 # Files to be removed in build directory
 clean-local:
 	@if test '@srcdir@' != '@builddir@'; then \
-		rm -rf $(builddir)/cs*.py; \
-		rm -rf $(builddir)/obsutils.py; \
-		rm -rf $(builddir)/modutils.py; \
-		rm -rf $(builddir)/calutils.py; \
-		rm -rf $(builddir)/ioutils.py; \
-		rm -rf $(builddir)/*.par; \
+		rm -rf $(top_builddir)/cscripts/cs*.py; \
+		rm -rf $(top_builddir)/cscripts/obsutils.py; \
+		rm -rf $(top_builddir)/cscripts/modutils.py; \
+		rm -rf $(top_builddir)/cscripts/calutils.py; \
+		rm -rf $(top_builddir)/cscripts/ioutils.py; \
+		rm -rf $(top_builddir)/cscripts/*.par; \
 	fi
-	rm -rf $(builddir)/*.pyc
-	rm -rf $(builddir)/__pycache__
+	rm -rf $(top_builddir)/cscripts/*.pyc
+	rm -rf $(top_builddir)/cscripts/__pycache__
 
 # Uninstall the cscripts Python module
 uninstall-local:
diff --git a/pyext/Makefile.am b/pyext/Makefile.am
index 2e627d7..1326dab 100755
--- a/pyext/Makefile.am
+++ b/pyext/Makefile.am
@@ -33,7 +33,7 @@ if WITH_PYTHON
 # shipped with the distribution of whether the wrappers have to be build
 # using swig
 if BUILD_WRAPPERS
-  wrapperdir = $(builddir)
+  wrapperdir = $(top_builddir)/pyext
 else
   wrapperdir = $(srcdir)
 endif
@@ -99,8 +99,8 @@ CLEAN_FILES = $(BUILT_SOURCES)
 swig: $(BUILT_SOURCES)
 
 # Rule for building Python wrappers using SWIG.
-ctools/tools.py: ctools/tools_wrap.cpp
-ctools/tools_wrap.cpp: ctools/tools.i
+$(wrapperdir)/ctools/tools.py: $(wrapperdir)/ctools/tools_wrap.cpp
+$(wrapperdir)/ctools/tools_wrap.cpp: ctools/tools.i
 	if $(SWIGCOMPILE) -MMD -MF "tools.Tpi" -o ctools/tools_wrap.cpp $<; \
 	then mv -f "tools.Tpi" "tools.Pi"; else rm -f "tools.Tpi"; exit 1; fi
 
@@ -168,11 +168,11 @@ CLEANFILES = $(CLEAN_FILES) $(DEPFILES)
 # Files to be removed in build directory
 clean-local:
 	rm -rf build
-	rm -rf $(builddir)/ctools/tools.py
-	rm -rf $(builddir)/ctools/c*.py
-	rm -rf $(builddir)/ctools/*.pyc
-	rm -rf $(builddir)/ctools/*_wrap.cpp
-	rm -rf $(builddir)/ctools/_tools.so
-	rm -rf $(builddir)/ctools/__pycache__
+	rm -rf $(top_builddir)/pyext/ctools/tools.py
+	rm -rf $(top_builddir)/pyext/ctools/c*.py
+	rm -rf $(top_builddir)/pyext/ctools/*.pyc
+	rm -rf $(top_builddir)/pyext/ctools/*_wrap.cpp
+	rm -rf $(top_builddir)/pyext/ctools/_tools.so
+	rm -rf $(top_builddir)/pyext/ctools/__pycache__
 
 endif # WITH_PYTHON
diff --git a/test/Makefile.am b/test/Makefile.am
index 40838be..5dc4f9e 100644
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -49,19 +49,19 @@ all-local:
 
 # Files to be removed in build directory
 clean-local:
-	rm -rf $(builddir)/*.fits
-	rm -rf $(builddir)/*.log
-	rm -rf $(builddir)/*.xml
-	rm -rf $(builddir)/*.eps
-	rm -rf $(builddir)/*.dat
-	rm -rf $(builddir)/*.reg
-	rm -rf $(builddir)/reports/*.xml
-	rm -rf $(builddir)/caldb
-	rm -rf $(builddir)/pfiles
-	rm -rf $(builddir)/prod3
-	rm -rf $(builddir)/csroot2caldb_*
-	rm -rf $(builddir)/csiactcopy_*
-	rm -rf $(builddir)/.DS_Store
+	rm -rf $(top_builddir)/test/*.fits
+	rm -rf $(top_builddir)/test/*.log
+	rm -rf $(top_builddir)/test/*.xml
+	rm -rf $(top_builddir)/test/*.eps
+	rm -rf $(top_builddir)/test/*.dat
+	rm -rf $(top_builddir)/test/*.reg
+	rm -rf $(top_builddir)/test/reports/*.xml
+	rm -rf $(top_builddir)/test/caldb
+	rm -rf $(top_builddir)/test/pfiles
+	rm -rf $(top_builddir)/test/prod3
+	rm -rf $(top_builddir)/test/csroot2caldb_*
+	rm -rf $(top_builddir)/test/csiactcopy_*
+	rm -rf $(top_builddir)/test/.DS_Store
 
 # Tests to be done on installed version
 if WITH_PYTHON