A 3D device, including: a first layer including first transistors, the first transistors interconnected by a first layer of interconnection; a second layer including second transistors, the second transistors overlaying the first layer of interconnection, where the first layer includes a first clock distribution structure, where the second layer includes a second clock distribution structure, where the device includes a Phase Lock Loop (“PLL”) circuit, where the second clock distribution structure is connected to the Phase Lock Loop (“PLL”) circuit, and where the second transistors are aligned to the first transistors with less than 200 nm alignment error.