Disclosed are systems and methods for bonding wafers by use of microwave energy. Various components that facilitate relatively quick and efficient bonding provided by microwave energy are disclosed. In certain embodiments, devices and methods for applying desirable compression to the wafers can be implemented. In certain embodiments, devices and methods for providing a controlled gas environment such as vacuum can be implemented. In certain embodiments, devices and methods for maintaining the integrity of microwave mode of operation during the bonding process can be implemented. In certain embodiments, devices and methods for increasing throughput of the bonding process can be implemented.