A system for separately handling different size FOUPs includes an end effector having a surface thereon for supporting a FOUP. The end effector and surface is configured to support different size FOUPs. A fixture or means for engaging and maintaining a FOUP, of different size FOUPs, included to position and maintain each of a different size FOUP on the end effector during transport thereof. A shelf is configured to receive each of said different size FOUPs. The end effector is thus capable of transporting either a first size FOUP or a second, smaller size FOUP.