In one embodiment, a method for removing native oxides from a substrate surface is provided which includes supporting a substrate containing silicon oxide within a processing chamber, generating a plasma of reactive species from a gas mixture within the processing chamber, cooling the substrate to a first temperature of less than about 65° C. within the processing chamber, and directing the reactive species to the cooled substrate to react with the silicon oxide thereon while forming a film on the substrate. The film usually contains ammonium hexafluorosilicate. The method further provides positioning the substrate in close proximity to a gas distribution plate, and heating the substrate to a second temperature of about 100° C. or greater within the processing chamber to sublimate or remove the film. The gas mixture may contain ammonia, nitrogen trifluoride, and a carrier gas.