1. A substrate transport system for moving substrates in a semiconductor manufacturing process, the substrate transport system comprising: at least one tunnel capable of being sealed for holding a sealed environment within the at least one tunnel, the at least one tunnel having a first end and a second end and a transport path extending between the first and second ends; at least one transport cart disposed within the at least one tunnel and configured to traverse at least a portion of the transport path, each of the at least one transport carts being configured to hold at least one substrate; at least one sealable workpiece handling module communicably coupled to one or more of the first and second ends of the at least one tunnel through a respective exchange zone port of the at least one tunnel; an equipment front end unit having an environment external to the sealed environment and communicably coupled to the at least one sealable workpiece handling module through a distinct exchange zone that is different and distinct from the equipment front end unit and coupled to an outside of the equipment front end unit so as to be disposed between, and coupled to, the equipment front end unit and the at least one sealable workpiece handling module, the exchange zone being persistently external to the sealed environment so that at least a portion of the exchange zone accommodating substrate exchange therein persistently shares the external environment of the equipment front end unit and the exchange zone is isolated by each respective exchange zone port from the sealed environment of the at least one tunnel; and at least one robotic arm configured to reach into at least the portion of the exchange zone persistently sharing the external environment of the equipment front end unit and indirectly transfer the at least one substrate therefrom to the at least one transport cart, the at least one robotic arm being located at one or more of the first and second ends for introducing the at least one substrate into the at least one tunnel, through the at least one sealable workpiece handling module and the respective exchange zone port, from the environment persistently external to the sealed environment.