A semiconductor device including: a first level including a plurality of first memory arrays, a plurality of first transistors, and a plurality of first metal layers; a second level disposed on top of the first level, where the second level includes a plurality of second memory arrays; and a third level disposed on top of the second level, where the third level includes a plurality of third transistors and a plurality of third metal layers, the third level is bonded to the second level, where the bonded includes oxide to oxide bonding regions and a plurality of metal to metal bonding regions, where the first level includes first filled holes (FFHs), where the second level includes second filled holes (SFHs), where the SFHs are aligned to the FFHs with a more than 1 nm but less than 40 nm alignment error, where the third level includes a plurality of Look-Up-Table circuits.