A 3D integrated circuit, the circuit including: a first level including a first wafer, the first wafer including a first crystalline substrate, a plurality of first transistors, and first copper interconnecting layers, where the first copper interconnecting layers at least interconnect the plurality of first transistors; and a second level including a second wafer, the second wafer including a second crystalline substrate, a plurality of second transistors, and second copper interconnecting layers, where the second copper interconnecting layers at least interconnect the plurality of second transistors, where the second level is bonded to the first level, where the bonded includes metal to metal bonding, where the bonded includes oxide to oxide bonding, and where at least one of the second transistors include a replacement gate.