Chemical vapor deposition (CVD) systems for forming layers on a substrate are disclosed. Embodiments of the system comprise at least two processing chambers that may be linked in a cluster tool. A first processing chamber provides a chamber having a controlled environmental temperature and pressure and containing a first environment for performing CVD on a substrate, and a second environment for contacting the substrate with a plasma; a substrate transport system capable of positioning a substrate for sequential processing in each environment, and a gas control system capable of maintaining isolation. A second processing chamber provides a CVD system. Methods of forming layers on a substrate comprise forming one or more layers in each processing chamber. The systems and methods are suitable for preparing Group III-V, Group II-VI or Group IV thin film devices.