1. A substrate transport system for moving a wafer 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; and at least one robotic arm configured to indirectly transfer substrates 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 substrates into the at least one tunnel from the an environment external to the sealed environment.