A method and apparatus for processing substrates using a multi-chamber processing system, or cluster tool, that has an increased system throughput, increased system reliability, improved device yield performance, a more repeatable wafer processing history (or wafer history), and a reduced footprint. The various embodiments of the cluster tool may utilize two or more robots that are configured in a parallel processing configuration to transfer substrates between the various processing chambers retained in the processing racks so that a desired processing sequence can be performed on the substrates. In one aspect, the parallel processing configuration contains two or more robot assemblies that are adapted to move in a vertical and horizontal directions, to access the various processing chambers retained in generally adjacently positioned processing racks. Generally, the various embodiments described herein are advantageous since each row or group of substrate processing chambers are serviced by two or more robots to allow for increased throughput and increased system reliability. Also, the various embodiments described herein are generally configured to minimize and control the particles generated by the substrate transferring mechanisms, to prevent device yield and substrate scrap problems that can affect the cost of ownership of the cluster tool. The flexible and modular architecture allows the user to configure the number of processing chambers, processing racks, and processing robots required to meet the throughput needs of the user.