An active layer wafer having a larger diameter is placed over a stationary supporting substrate wafer having a smaller diameter. A pusher plate is pressed against an orientation flat of the larger wafer to move the wafer substantially in the horizontal direction. In the course of the pressing operation, the pusher plate is also pressed against the orientation flat of the smaller wafer so as to move the two wafers together. Then, as a result of each of the cut sections for alignment of the wafer being pressed against an aligning plate, the larger wafer and the smaller wafer can be bonded to each other with their centerlines and orientation flats aligned with respect to each other.