Methods of processing a substrate are provided herein. In some embodiments, a method of processing a substrate disposed in a processing chamber includes: (a) depositing a layer of material on a substrate by exposing the substrate to a first reactive species generated from a remote plasma source and to a first precursor, wherein the first reactive species reacts with the first precursor; and (b) treating all, or substantially all, of the deposited layer of material by exposing the substrate to a plasma generated within the processing chamber from a second plasma source; wherein at least one of the remote plasma source or the second plasma source is pulsed to control periods of depositing and periods of treating.