The present invention is a wafer transfer system that transports individual wafers between chambers within an isolated environment. In one embodiment, a wafer is transported by a wafer shuttle that travel within a transport enclosure. The interior of the transport enclosure is isolated from the atmospheric conditions of the surrounding wafer fabrication facility. Thus, an individual wafer may be transported throughout the wafer fabrication facility without having to maintain a clean room environment for the entire facility. The wafer shuttle may be propelled by various technologies, such as, but not limited to, magnetic levitation or air bearings. The wafer shuttle may also transport more than one wafer simultaneously. The interior of the transport enclosure may also be under vacuum, gas-filled, or subject to filtered air.