An apparatus and method for handling and/or pre-processing microelectronic workpieces. In one embodiment, the apparatus includes an input/output station configured to removably receive a plurality of microelectronic workpieces at an input/output location, a transfer station, and a first transfer device that moves the microelectronic workpieces directly between the input/output location and the transfer station. A second transfer device moves the microelectronic workpieces directly from the transfer station to at least one process station. The transfer station can include a pre-process station configured to identify and/or align the microelectronic workpieces. The apparatus can further include a storage station configured to support a plurality of microelectronic workpieces and can be positioned to at least partially overlap the pre-process station.