Methods for removing silicon nitride and elemental silicon during contact preclean process involve converting these materials to materials that are more readily etched by fluoride-based etching methods, and subsequently removing the converted materials by a fluoride-based etch. Specifically, silicon nitride and elemental silicon may be treated with an oxidizing agent, e.g., with an oxygen-containing gas in a plasma, or with O2 or O3 in the absence of plasma to produce a material that is more rich in Si—O bonds and is more easily etched with a fluoride-based etch. Alternatively, silicon nitride or elemental silicon may be doped with a number of doping elements, e.g., hydrogen, to form materials which are more easily etched by fluoride based etches. The methods are particularly useful for pre-cleaning contact vias residing in a layer of silicon oxide based material because they minimize the unwanted increase of critical dimension of contact vias.