The present invention generally provides an apparatus and method for processing and transferring substrates in a multi-chamber processing system that has the capability of receiving and performing single substrate processing steps performed in parallel, while using the many favorable aspects of batch processing. Embodiments of the invention described herein are adapted to maximize system throughput, reduce system cost, reduce cost per substrate during processing, increase system reliability, improve the device yield on the processed substrates, and reduce system footprint. In one embodiment, the cluster tool is adapted to perform a wet/clean process sequence in which various substrate cleaning processes are performed on a substrate in the cluster tool.