A method of manufacturing a semiconductor structure is provided. The method includes forming a hard mask pattern on a semiconductor substrate, wherein the hard mask pattern covers active regions; forming a trench in the semiconductor substrate within an opening defined by the hard mask pattern; filling the trench with a dielectric material, resulting in a trench isolation feature; performing an ion implantation to the trench isolation feature using the hard mask pattern to protect active regions of the semiconductor substrate; and removing the hard mask pattern after the performing of the ion implantation.