A method of making a semiconductor device includes etching a substrate to define a trench in a substrate, wherein the trench is adjacent to an active region in the substrate, and etching the substrate includes patterning a mask. The method further includes partially removing the mask to expose a first portion of the active region, wherein the first portion extends a first distance from the trench. The method further includes depositing a dielectric material to fill the trench and cover the first portion of the active region. The method further includes removing the mask, wherein the removing of the mask includes maintaining the dielectric material covering the first portion of the active region. The method further includes forming a gate structure over the active region and over the dielectric material.