A method includes determining a first offset between a first alignment mark on a first side of a first wafer and a second alignment mark on a second side of the first wafer; aligning the first alignment mark of the first wafer to a third alignment mark on a first side of a second wafer, which includes detecting a location of the second alignment mark of the first wafer; determining a location of the first alignment mark of the first wafer based on the first offset and the location of the second alignment mark of the first wafer; and, based on the determined location of the first alignment mark, repositioning the first wafer to align the first alignment mark to the third alignment mark; and bonding the first side of the first wafer to the first side of the second wafer to form a bonded structure.