A method and system for processing a substrate includes providing the substrate in a process chamber, where the substrate contains an oxide layer formed thereon, exciting a hydrogen-containing gas in a remote plasma source coupled to the process chamber, and exposing the substrate to a flow of the excited hydrogen-containing gas at a first substrate temperature lower than about 900° C. to remove the oxide layer from the substrate. The substrate is then maintained at a second temperature different than the first substrate temperature, and a silicon-containing film is formed on the substrate at the second substrate temperature.