A method of manufacturing a die stack, comprising: forming a plurality of through-wafer vias from a first surface of a first die; forming a plurality of alignment recesses from the first surface of the first die; filling each of the through-wafer vias with a conductive material to form filled through-wafer vias; wherein the step of forming the plurality of through-wafer vias comprises, as an initial step, forming a plurality of openings to a first depth of the first die, and the step of forming a plurality of alignment recesses comprises forming the plurality of alignment recesses to a second depth at least or greater than the first depth; back grinding a second surface of the first die opposite the first surface and etching the second surface of the first die, such that the conductive material extends beyond the second surface of the first die and the alignment recesses are exposed at the second surface of the first die: forming a plurality of alignment protrusions on a first surface of a second die; and stacking one of the first and second die (100, 112) onto the other of the first and second die, such that each of the plurality of alignment protrusions engages a respective one of the plurality of alignment recesses at the second surface of the first die (100, 200, 302, 400, 504) such that each of the plurality of filled through-wafer vias of the first die is vertically aligned with a respective one of a plurality of bond pads on the first surface of the second die, wherein the plurality of bond pads of the second die align with the conductive material of the plurality of filled through-wafer vias; and forming a plurality of electrical contacts wherein each electrical contact of the plurality of electrical contacts is formed between each of the plurality of filled through-wafer vias of the first die and a respective one of the plurality of bond pads of the second die subsequent to stacking one of the first and second die (100, 112) onto the other of the first and second die (100, 112) when the plurality of recesses engage the plurality of protrusions. forming a plurality of through-wafer vias from a first surface of a first die; forming a plurality of alignment recesses from the first surface of the first die; filling each of the through-wafer vias with a conductive material to form filled through-wafer vias; wherein the step of forming the plurality of through-wafer vias comprises, as an initial step, forming a plurality of openings to a first depth of the first die, and the step of forming a plurality of alignment recesses comprises forming the plurality of alignment recesses to a second depth at least or greater than the first depth; back grinding a second surface of the first die opposite the first surface and etching the second surface of the first die, such that the conductive material extends beyond the second surface of the first die and the alignment recesses are exposed at the second surface of the first die: forming a plurality of alignment protrusions on a first surface of a second die; and stacking one of the first and second die (100, 112) onto the other of the first and second die, such that each of the plurality of alignment protrusions engages a respective one of the plurality of alignment recesses at the second surface of the first die (100, 200, 302, 400, 504) such that each of the plurality of filled through-wafer vias of the first die is vertically aligned with a respective one of a plurality of bond pads on the first surface of the second die, wherein the plurality of bond pads of the second die align with the conductive material of the plurality of filled through-wafer vias; and forming a plurality of electrical contacts wherein each electrical contact of the plurality of electrical contacts is formed between each of the plurality of filled through-wafer vias of the first die and a respective one of the plurality of bond pads of the second die subsequent to stacking one of the first and second die (100, 112) onto the other of the first and second die (100, 112) when the plurality of recesses engage the plurality of protrusions. forming a plurality of alignment protrusions on a first surface of a second die; and stacking one of the first and second die (100, 112) onto the other of the first and second die, such that each of the plurality of alignment protrusions engages a respective one of the plurality of alignment recesses at the second surface of the first die (100, 200, 302, 400, 504) such that each of the plurality of filled through-wafer vias of the first die is vertically aligned with a respective one of a plurality of bond pads on the first surface of the second die, wherein the plurality of bond pads of the second die align with the conductive material of the plurality of filled through-wafer vias; and forming a plurality of electrical contacts wherein each electrical contact of the plurality of electrical contacts is formed between each of the plurality of filled through-wafer vias of the first die and a respective one of the plurality of bond pads of the second die subsequent to stacking one of the first and second die (100, 112) onto the other of the first and second die (100, 112) when the plurality of recesses engage the plurality of protrusions.