A dual track substrate handling and processing system includes an entrance load lock station, an exit load lock station and a plurality of substrate processing stations, all positioned above a transfer vacuum chamber. The load lock station and each processing station are configured to hold two vertically oriented workpieces. A transport system conveys workpieces two at a time from parallel input cassettes to the entrance load lock station. The transport system includes a transport assembly that simultaneously advances two workpieces from each station to the next station; thus workpieces are processed two at a time in the same environment in each processing station and system throughput is correspondingly increased.