Provided are methods and systems for removing a native silicon oxide layer on a wafer. In a non-sequential approach, a wafer is provided with a native silicon oxide layer on a polysilicon layer. An etchant including a hydrogen-based species and a fluorine-based species is introduced, exposed to a plasma, and flowed onto the wafer at a relatively low temperature. The wafer is then heated to a slightly elevated temperature to substantially remove the native oxide layer. In a sequential approach, a wafer is provided with a native silicon oxide layer. A first etchant including a hydrogen-based species and a fluorine-based species is flowed onto the wafer. Then the wafer is heated to a slightly elevated temperature, a second etchant is flowed towards the wafer, and the second etchant is exposed to a plasma to complete the removal of the native silicon oxide layer and to initiate removal of another layer such as a polysilicon layer.