Embodiments generally provide an apparatus and method for processing substrates using a multi-chamber processing system (e.g., a cluster tool) that has an increased system throughput, increased system reliability, substrates processed in the cluster tool have a more repeatable wafer history, and also the cluster tool has a smaller system footprint. In one embodiment, the cluster tool is adapted to perform a track lithography process in which a substrate is coated with a photosensitive material, is then transferred to a stepper/scanner, which exposes the photosensitive material to some form of radiation to form a pattern in the photosensitive material, which is then removed in a developing process completed in the cluster tool. In track lithography type cluster tools, since the chamber processing times tend to be rather short, and the number of processing steps required to complete a typical track system process is large, a significant portion of the time it takes to process a substrate is taken up by the processes of transferring the substrates in a cluster tool between the various processing chambers. In one embodiment of the cluster tool, the cost of ownership, is reduced by grouping substrates together and transferring and processing the substrates in groups of two or more to improve system throughput, and reduces the number of moves a robot has to make to transfer a batch of substrates between the processing chambers, thus reducing wear on the robot and increasing system reliability. In one aspect of the invention, the substrate processing sequence and cluster tool are designed so that the substrate transferring steps performed during the processing sequence are only made to chambers that will perform the next processing step in the processing sequence. Embodiments also provide for a method and apparatus that are used to improve the coater chamber, the developer chamber, the post exposure bake chamber, the chill chamber, and the bake chamber process results. 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.