An apparatus provided with a wafer processing chamber that houses a wafer supporting mechanism supporting a wafer and is used to irradiate the wafer supported by the wafer supporting mechanism with an ion beam and a transport mechanism housing chamber that houses a transport mechanism provided underneath the wafer processing chamber and used for moving the wafer supporting mechanism in a substantially horizontal direction, wherein an aperture used for moving the wafer supporting mechanism along with a coupling member coupling the wafer supporting mechanism to the transport mechanism is formed in the direction of movement of the transport mechanism in a partition wall separating the wafer processing chamber from the transport mechanism housing chamber.