The present invention relates a physical vapor deposition (PVD) system. e.g. a planetary system, for forming one or more layers of a coating material on a substrate and for treating, or modifying, the substrate surface, which can include the surface of the substrate or a deposited layer of coating material thereon. The PVD system includes a single vacuum (or process) chamber having an ion source and at least one PVD source of the coating material. The ion source, such as a linear ion source, is configured to emit a beam of energetic particles at a substrate for surface modification of the substrate surface, for example, to provide film densification, etching, cleaning, surface smoothing, and/or oxidation thereof. The PVD source(s) of the coating material deposits one or more layers of coating material(s) on the substrate. The uniformity of substrate surface modification and the thickness uniformity of the deposited layers can be maintained by velocity profiling of the rotating substrate within the vacuum chamber.