In an embodiment, a wafer bonding system includes a chamber, a gas inlet and a gas outlet configured to control a pressure of the chamber to be in a range from 1×10−2 mbar to 1520 torr, a first wafer chuck having a first surface to support a first wafer, and a second wafer chuck having a second surface to support a second wafer, the second surface being opposite the first surface, the second wafer chuck and the first wafer chuck being movable relative to each other, wherein the second surface that supports the second wafer is divided into zones, wherein a vacuum pressure of each zone is controlled independently of other zones.