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. The processing chambers may be, for example, physical vapor deposition (PVD) or sputtering chambers, plasma enhanced chemical vapor deposition (PECVD) chambers, low pressure chemical vapor deposition (LPCVD) chambers, hot wire chemical vapor deposition (HWCVD) chambers, plasma nitridation (DPN) chambers, ion implant / doping chambers, atomic layer deposition (ALD) chambers, plasma etching chambers, annealing chambers, rapid thermal oxidation (RTO) chambers, rapid thermal annealing (RTA) chambers, substrate reorientation chambers, laser annealing chambers, and / or plasma cleaning stations. 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.