The present invention generally provides a batch substrate processing system, or cluster tool, for in-situ processing of a film stack used to form regions of a solar cell device. In one configuration, the film stack formed on each of the substrates in the batch contains one or more silicon-containing layers and one or more metal layers that are deposited and further processed within the various chambers contained in the substrate processing system. In one embodiment, a batch of solar cell substrates is simultaneously transferred in a vacuum or inert environment to prevent contamination from affecting the solar cell formation process.