A method and apparatus for the deposition of thin films is described. In embodiments, systems and methods for epitaxial thin film formation are provided, including systems and methods for forming binary compound epitaxial thin films. Methods and systems of embodiments of the invention may be used to form direct bandgap semiconducting binary compound epitaxial thin films, such as, for example, GaN, InN and AlN, and the mixed alloys of these compounds, e.g., (In, Ga)N, (Al, Ga)N, (In, Ga, Al)N. Methods and apparatuses include a multistage deposition process and system which enables rapid repetition of sub-monolayer deposition of thin films.