A semiconductor device has a first semiconductor wafer. The first semiconductor wafer is singulated to provide a first wafer section including at least one first semiconductor die or a plurality of first semiconductor die. The first wafer section is a fractional portion of the first semiconductor wafer. An edge support structure is formed around the first wafer section. A second wafer section includes at least one second semiconductor die. The second wafer section can be an entire second semiconductor wafer. The first semiconductor die is a first type of semiconductor device and the second semiconductor die is a second type of semiconductor device. An alignment opening is formed through the first wafer section and second wafer section with a light source projected through the opening. The first wafer section is bonded to the second wafer section with the first semiconductor die aligned with the second semiconductor die.