A method of aligning two wafers during a bonding process includes aligning a first wafer having a plurality of alignment markings with a second wafer having a plurality of alignment markings. The method further includes placing a plurality of flags between the first wafer and the second wafer. The method further includes detecting movement of the plurality of flags with respect to the first wafer and the second wafer using at least one sensor. The method further includes determining whether the wafers remain aligned within an alignment tolerance based on the detected movement of the plurality of flags relative to the first wafer and the second wafer.