An automated processing system has an indexer bay perpendicularly aligned with a process bay within a clean air enclosure. An indexer in the indexer bay provides stocking or storage for work in progress wafers or articles. Process chambers are located in the process bay. A transfer robot moves wafers from a pod unsealed at a docking station into a carrier at a transfer station. The carrier has tapered or stepped outside surfaces engaging corresponding inside surfaces on a rotor within a process chamber. A process robot moves between the indexer bay and process bay to carry wafers to and from the process chambers. The process robot has a robot arm vertically moveable along a lift rail. Wafers are carried offset from the robot arm, to better avoid contamination. The automated system is compact and requires less clean room floor space.