diff --git a/.flake8 b/.flake8
index 7573178348318db0afa26b291c9dc16a997f5a79..92279a97ca94a993667388338000cd33fdb78161 100644
--- a/.flake8
+++ b/.flake8
@@ -38,10 +38,6 @@ per-file-ignores =
     # Ignore unused imports in __init__.py
     __init__.py: F401
     # These files will be fixed later
-    r/*:F401
-    cmake/*:F401
-    paddle/*:F401
-    tools/*:F401
     python/paddle/signal.py:F401
     python/paddle/common_ops_import.py:F401
     python/paddle/check_import_scipy.py:F401