A semiconductor device is manufactured by forming trenches in a substrate and selectively performing Plasma Ion Immersion Implantation and Deposition (PIIID) on a subset of the trenches in the substrate. The PIIID may be performed on only a portion of a surface of at least one of the trenches in the substrate. Semiconductor devices can include a semiconductor substrate having first, second and third trenches therein, and an oxide liner layer that fully lines the first trenches, that does not line the second trenches and that partially lines the third trenches.