A computer readable medium is provided that is encoded with a program comprising instructions for performing a method for fabricating a 3D integrated circuit structure. Provided are an interface wafer including a first wiring layer and through-silicon vias, and a first active circuitry layer wafer including active circuitry. The first active circuitry layer wafer is bonded to the interface wafer. Then, a first portion of the first active circuitry layer wafer is removed such that a second portion remains attached to the interface wafer. A stack structure including the interface wafer and the second portion of the first active circuitry layer wafer is bonded to a base wafer. Next, the interface wafer is thinned so as to form an interface layer, and metallizations coupled through the through-silicon vias in the interface layer to the first wiring layer are formed on the interface layer.