A 3D semiconductor device, the device including: a first layer including first transistors each including a silicon channel; a second layer including second transistors each including a silicon channel, the second layer overlaying the first transistors, where at least one of the second transistors is at least partially self-aligned to at least one of the first transistors; and a third layer including third transistors each including a single crystal silicon channel, the third layer underlying the first transistors, where a plurality of the third transistors form a logic circuit, and where the logic circuit is aligned to the second transistors with less than 200 nm alignment error, where the first layer thickness is less than one micron, and where the first transistor is a junction-less transistor.