A 3D semiconductor device including: a first structure including first single crystal transistors; a second structure including second single crystal transistors, the second structure overlaying the first single crystal transistors, where at least one of the second single crystal transistors is at least partially self-aligned to at least one of the first single crystal transistors; and at least one thermal conducting path from at least one of the first single crystal transistors and second single crystal transistors to an external surface of the device.