Embodiments generally provide an apparatus and method for processing substrates using a multi-chamber processing system (e.g., a cluster tool). In one embodiment, the cluster tool is adapted to perform a track lithography process in which a photosensitive material is applied to a substrate, patterned in a stepper/scanner, and then removed in a developing process completed in the cluster tool. In one embodiment of the cluster tool, substrates are grouped together in groups of two or more for transfer or processing to improve system throughput, reduce the number of moves a robot has to make to transfer a batch of substrates between the processing chambers, and thus increase system reliability. Embodiments also provide for a method and apparatus that are used to increase the reliability of the substrate transfer process to reduce system down time.