A method of forming a semiconductor device includes patterning a photoresist layer formed over a homogeneous semiconductor device layer to be etched; subjecting the semiconductor device to an implant process that selectively implants a sacrificial etch stop layer that is self-aligned in accordance with locations of features to be etched within the homogeneous semiconductor device layer, and at a desired depth for the features to be etched; etching a feature pattern defined by the patterned photoresist layer into the homogenous semiconductor device layer, stopping on the implanted sacrificial etch stop layer; and removing remaining portion of the implanted sacrificial etch stop layer prior to filling the etched feature pattern with a fill material.