Abstract: A system and methods for handling semiconductor wafers and dummy wafers in semiconductor process equipment such as an ion implanter. Tray assemblies are provided, each of which is adapted for releasably holding and automatically aligning a standard semiconductor wafer cassette next to a dedicated dummy-wafer cassette. The dummy wafers are used to complete a full load of wafers when there are insufficient wafers in the standard cassette. The trays are mounted on the paddles of a load lock carousel, which indexes the trays to an unloading/loading station. There, an indexer assembly picks up and indexes the tray so that the standard and dummy wafers can be selectively lifted by a vertical transport mechanism to a pivotal wafer chuck for transfer into the process equipment.