A method of manufacturing a semiconductor device is providing, which includes forming a trench in a semiconductor substrate, forming an oxide layer over sidewalls and over a bottom side of the trench, performing an ion implantation process, forming a cover layer, and patterning the covering layer, thereby forming an uncovered area and a covered area of the oxide layer, respectively. The method further includes performing an isotropic etching process thereby removing portions of the uncovered area of the oxide layer and removing a part of a surface portion of the covered area adjacent to the uncovered portions, and removing remaining portions of the covering layer.