Chemical and physical modifications of photoresist and BARC during plasma patterning process on HKMG structure can cause residual defects and yield loss that challenges the subsequent wet cleaning process to resolve this issue. The chemical behavior of materials post dry etching and wet clean was systematically studied by various surface analytical techniques including STEM-EELS, XPS and AES. With a greater understanding of the etching and clean mechanisms, a combined aqueous/solvent cleaning method was developed and tested on a spin clean tool to effectively clean etching by-products. A significant improvement of yield with the application of the new cleaning approach has been observed.