An method of fabricating the gate structure comprises: sequentially depositing and patterning a dummy oxide layer and a dummy gate electrode layer on a substrate; surrounding the dummy oxide layer and the dummy gate electrode layer with a nitrogen-containing dielectric layer and an interlayer dielectric layer; removing the dummy gate electrode layer; removing the dummy oxide layer by exposing a surface of the dummy oxide layer to a vapor mixture comprising NH3 and a fluorine-containing compound at a first temperature; heating the substrate to a second temperature to form an opening in the nitrogen-containing dielectric layer; depositing a gate dielectric; and depositing a gate electrode.