Abstract: Embodiments of the invention provide methods for processing substrates within a substrate processing system. In one embodiment, the method provides depositing a material on a substrate within a vapor deposition chamber coupled to a buffer chamber contained within a mainframe while maintaining a pressure of about 1×10?6 Torr or lower within a transfer chamber contained within the mainframe. The method further includes transferring the substrate from the vapor deposition chamber to the buffer chamber by a substrate handling robot while flowing a gas into the buffer chamber, evacuating the vapor deposition chamber, and maintaining a greater internal pressure within the buffer chamber than in the vapor deposition chamber. In some embodiments, the method includes transferring the substrate from the transfer chamber to a PVD chamber coupled to the transfer chamber by another substrate handling robot and depositing another material on the substrate within the PVD chamber.