Methods for processing a substrate are described herein. Methods can include positioning a substrate with an exposed surface comprising a silicon oxide layer in a processing chamber, biasing the substrate, treating the substrate to roughen a portion of the silicon oxide layer, heating the substrate to a first temperature, exposing the exposed surface of the substrate to ammonium fluoride to form one or more volatile products while maintaining the first temperature, and heating the substrate to a second temperature, which is higher than the first temperature, to sublimate the volatile products.