an interlock system prevents collision of handling equipment and damage to wafers in an automated wafer transport apparatus during manual control by an operator . sensors are used to sense when wafer transport arms and wafer stage are both in their home positions . a controller is responsive to the sensors for operating the lockout system such that attempted activation of the transport arm by the operator is locked out unless both the stage and the arms are in their home positions . the lockout system preferably comprises normally closed electrical relays .