A method for making a film stack containing one or more silicon-containing layers and one or more metal-containing layers and a substrate processing system for forming the film stack on a substrate are provided. The substrate processing system includes one or more transfer chambers coupled to one or more load lock chambers and two or more different types of process chambers. The two or more types of process chambers are used to deposit the one or more silicon-containing layers and the one or more metal-containing layers in the same substrate processing system without breaking the vacuum, taking the substrate out of the substrate processing system to prevent surface contamination, oxidation, etc., such that additional cleaning or surface treatment steps can be eliminated. The substrate processing system is configured to provide high throughput and compact footprint for in-situ substrate processing and carry out different types of processes.