A thin layer of silicon is deposited within a high aspect ratio feature to provide a template for selective deposition of oxide therein. In accordance with one embodiment, amorphous silicon is deposited within a shallow trench feature overlying an oxide liner grown therein. After exposure to sputtering to remove the amorphous silicon from outside of the trench, oxide is selectively deposited over the amorphous silicon to fill the trench from the bottom up without voids, thereby creating a shallow trench isolation (STI) structure. Deposition of the amorphous silicon or other silicon containing layers allows the selective oxide deposition step to be integrated with a thermally-grown oxide trench liner.