Embodiments described herein provide methods for removing native oxide surfaces on substrates while simultaneously passivating the underlying substrate surface. In one embodiment, a method is provided which includes positioning a substrate containing an oxide layer within a processing chamber, adjusting a first temperature of the substrate to about 80° C. or less, generating a cleaning plasma from a gas mixture within the processing chamber, such that the gas mixture contains ammonia and nitrogen trifluoride having an NH3/NF3 molar ratio of about 10 or greater, and condensing the cleaning plasma onto the substrate. A thin film, containing ammonium hexafluorosilicate, is formed in part, from the native oxide during a plasma clean process. The method further includes heating the substrate to a second temperature of about 100° C. or greater within the processing chamber while removing the thin film from the substrate and forming a passivation surface thereon.