A substrate processing system particularly suitable for fabricating solar cells. The system has a front end module transporting cassettes, each cassette holding a preset number of substrates therein; a loading module coupled to the front end module and having mechanism for loading substrates from the cassettes onto carriers; and a plurality of processing chambers coupled to each other in series, each having tracks for transporting the carriers directly from one chamber to the next; wherein selected chambers of the plurality of processing chambers comprise at least one combination source having a sputtering module and an evaporation module arranged linearly in the direction of travel of the carriers.