Structure and methods of forming stacked semiconductor chips are described. In one embodiment, a method of forming a semiconductor chip includes forming an opening for a through substrate via from a top surface of a first substrate. The sidewalls of the opening are lined with an insulating liner and the opened filled with a conductive fill material. The first substrate is etched from an opposite bottom surface to form a protrusion, the protrusion being covered with the insulating liner. A resist layer is deposited around the protrusion to expose a portion of the insulating liner. The exposed insulating liner is etched to form a sidewall spacer along the protrusion.