Abstract: The present invention relates in a system and method for handling and processing substrates for magnetic and optical media and other types of substrates, such as wafers and lenses, requiring thin-film coatings. The system includes input and output locks which act as buffers between atmosphere and the high vacuum within the system and a transfer/main chamber which is comprised of a variable number of chamber modules. The system also includes various mechanisms for moving the substrates and the substrate carriers within the system, and components for dealing with the process and environmental requirements.