A method for making a film stack containing 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 at least one transfer chamber coupled to at least one load lock chamber, at least one first physical vapor deposition (PVD) chamber configured to deposit a first material layer on a substrate, and at least one second PVD chamber for in-situ deposition of a second material layer over the first material layer within the same substrate processing system without breaking the vacuum or taking the substrate out of the substrate processing system to prevent surface contamination, oxidation, etc. The substrate processing system is configured to provide high throughput and compact footprint for in-situ sputtering of different material layers in designated PVD chambers.