A substrate processing apparatus (10, 10', 18A, 18B) comprising: a transport chamber (18, 18', 602-624, 716) capable of having a controlled atmosphere therein; at least one first substrate holding module (16, 20, 301, 302) for holding a substrate (148, 506, 702A, 702B), the at least one first holding module being communicably connected to the transport chamber for allowing transfer of the substrate between the at least one first holding module and the transport chamber; a transport vehicle (22, 122A, 122B, 229, 406, 700, 760, 1557, 1557', 1557") movably mounted in the transport chamber, the vehicle having a base (502, 1558, 1558') and a substrate transfer arm (22A, 504, 536, 538, 1577, 1577") that is movably jointed and movably mounted to the base; a second module (16, 20, 301, 302) capable of holding the substrate and communicably connected to the transport chamber for transferring the substrate therebetween; where the transport chamber defines a linear travel slot for the vehicle, the at least one first holding module being located on one side of the slot, and the arm having articulation for moving a substrate to opposite sides of the slot allowing the second module to be selectably connected to the transport chamber on either side of the slot, wherein the transport vehicle can effect transfer of the substrate between the transport chamber and both the at least one first holding module and the second module, characterized in that a linear motor is connected to the transport chamber for driving the transport vehicle and the linear motor is connected to the arm for rotating the arm relative to the base and articulating the arm in opposite directions. a transport chamber (18, 18', 602-624, 716) capable of having a controlled atmosphere therein; at least one first substrate holding module (16, 20, 301, 302) for holding a substrate (148, 506, 702A, 702B), the at least one first holding module being communicably connected to the transport chamber for allowing transfer of the substrate between the at least one first holding module and the transport chamber; a transport vehicle (22, 122A, 122B, 229, 406, 700, 760, 1557, 1557', 1557") movably mounted in the transport chamber, the vehicle having a base (502, 1558, 1558') and a substrate transfer arm (22A, 504, 536, 538, 1577, 1577") that is movably jointed and movably mounted to the base; a second module (16, 20, 301, 302) capable of holding the substrate and communicably connected to the transport chamber for transferring the substrate therebetween; where the transport chamber defines a linear travel slot for the vehicle, the at least one first holding module being located on one side of the slot, and the arm having articulation for moving a substrate to opposite sides of the slot allowing the second module to be selectably connected to the transport chamber on either side of the slot, wherein the transport vehicle can effect transfer of the substrate between the transport chamber and both the at least one first holding module and the second module, characterized in that a linear motor is connected to the transport chamber for driving the transport vehicle and the linear motor is connected to the arm for rotating the arm relative to the base and articulating the arm in opposite directions.