A method for depositing material on a substrate is described. The method comprises maintaining a reduced-pressure environment around a substrate holder for holding a substrate having a surface, and holding the substrate securely within the reduced-pressure environment. Additionally, the method comprises providing to the reduced-pressure environment a gas cluster ion beam (GCIB) from a pressurized gas mixture, accelerating the GCIB, and irradiating the accelerated GCIB onto at least a portion of the surface of the substrate to form a thin film. In one embodiment, the pressurized gas mixture comprises a silicon-containing specie and at least one of a nitrogen-containing specie or a carbon-containing specie for forming a thin film containing silicon and at least one of nitrogen or carbon. In another embodiment, the gas mixture comprises a metal-containing specie for forming a thin metal-containing film. In yet another embodiment, the pressurized gas mixture comprises a fluorocarbon-containing specie for forming a thin fluorocarbon-containing film.