A vacuum pumping system and method in conjunction with a sputter reactor having a vacuum-pumped magnetron chamber sealed to the target backing plate. A main sputter chamber is vacuum sealed to the target front and cryo pumped. A bypass conduit and valve connect the magnetron and main chambers. A mechanical roughing pump connected to the magnetron chamber pumps the main chamber through the bypass conduit to less than 1 Torr before the bypass valve is closed and the cryo pump is opened and thereafter continues to pump the magnetron chamber to reduce the pressure differential across the target. A pressure differential switch connected across the bypass valve immediately open it whenever the pressure differential exceeds a limit, such as 20 Torr, for example when there is a leak or an electrical failure. The bypass conduit is also used in a venting procedure.