A 3D semiconductor device, the device including: a first single crystal layer including a plurality of first transistors; at least one metal layer interconnecting the first transistors, a portion of the first transistors forming a plurality of logic gates; a plurality of second transistors overlaying the first single crystal layer; at least one connection from the plurality of first transistors to a plurality of through silicon vias (TSVs); a plurality of third transistors overlaying the plurality of second transistors, where the plurality of second transistors are self-aligned to the plurality of third transistors having been processed following the same lithography step; and a first memory array and a second memory array, where the first memory array includes the plurality of second transistors and the second memory array includes the plurality of third transistors.