A substrate cleaning and drying system includes a cleaning station, a drying station positioned adjacent the cleaning station, a cleaner robot to transfer a substrate from the cleaning station to the drying station, an aligner stage adjacent to the drying station, a robot arm rotatable between a substantially vertical first position for receiving the substrate from the drying station and a substantially horizontal second position for releasing the substrate onto the aligner stage, and a factory interface robot to transfer a substrate from the aligner stage into a factory interface module while in a horizontal orientation. The aligner stage includes a rotatable support to hold the substrate in a substantially horizontal orientation and to rotate the substrate to a desired orientation.