A 3D semiconductor device, including: a first layer including first transistors; a first interconnection layer interconnecting the first transistors and includes aluminum or copper; a second layer including second transistors; where the second transistors are aligned to the first transistors with a less than 40 nm alignment error, and where the second layer is overlying the first interconnection layer, and where at least one of the second transistors has a back-bias structure designed to modify the performance of at least one of the second transistors.