The present invention provides a method of in-situ cleaning polymers from holes on a semiconductor wafer and in-situ removing the silicon nitride layer. The semiconductor wafer comprising a substrate, a silicon nitride (Si3N4) layer on the substrate, a silicon oxide (SiO2) layer on the silicon nitride layer, and a photo-resist layer on the silicon oxide layer. The silicon oxide layer and the photo-resist layer have a hole extending down to the silicon nitride layer. The hole contains polymer left after etching of the silicon oxide layer. The method comprises performing a in-situ plasma ashing process by injecting oxygen (O2) and argon (Ar) to completely remove the photo-resist layer and the polymer remaining within the hole. Subsequently, the silicon nitride layer was removed in the same chamber. The flow rate of O2 is maintained between 50˜2000 sccm (standard cubic centimeter per minute) and the flow rate of Ar is maintained between 50˜500 sccm.