diff --git a/pisi/actionsapi/libtools.py b/pisi/actionsapi/libtools.py
index dfc992e6..c60c3c9b 100644
--- a/pisi/actionsapi/libtools.py
+++ b/pisi/actionsapi/libtools.py
@@ -43,8 +43,9 @@ def gnuconfig_update():
     for root, dirs, files in os.walk(os.getcwd()):
         for file in files:
             if file in ['config.sub', 'config.guess']:
-                if os.path.islink(file):
-                    unlink(file)
+                targetFile = os.path.join(root, file)
+                if os.path.islink(targetFile):
+                    unlink(targetFile)
                 copy('/usr/share/gnuconfig/%s' % file, join_path(root, file))
                 ctx.ui.info(_('GNU Config Update Finished.'))