A method of wafer bonding includes bonding a wafer to a carrier in a bonding system. The method further includes measuring thickness profile of the bonded wafer. The method further includes modifying surface contours of at least one of an upper plate or a lower plate of the bonding system during a bonding operation to improve planarity of bonded wafers based on the measured thickness profile, wherein modifying the surface contours of at least one of the upper plate or the lower plate comprises modifying the surface contours using a plurality of height adjusters.