A 3D semiconductor device, the device including: a first single crystal layer including a plurality of first transistors and a first metal layer, where the first metal layer includes interconnecting the first transistors forming, at least in part a plurality of logic gates; a plurality of second transistors overlaying, at least in part the first single crystal layer; a plurality of third transistors overlaying, at least in part the second transistors; a second metal layer overlaying, at least in part the third transistors; Input/Output pads to provide connection to external devices, a local power grid to distribute power to the logic gates, where the third transistors are aligned to the first transistors with less than 40 nm misalignment, where the first single crystal layer includes a Phase Lock Loop (“PLL”) structure connected to at least one of the Input/Output pads, where a memory cell includes at least one of the third transistors.