A system and associated process for vapor deposition of a thin film layer on a photovoltaic (PV) module substrate is includes establishing a vacuum chamber and introducing the substrates individually into the vacuum chamber. A conveyor system is operably disposed within the vacuum chamber and is configured for conveying the substrates in a serial arrangement through a vapor deposition apparatus within the vacuum chamber at a controlled constant linear speed. A post-heat section is disposed within the vacuum chamber immediately downstream of the vapor deposition apparatus in the conveyance direction of the substrates. The post-heat section is configured to maintain the substrates conveyed from the vapor deposition apparatus in a desired heated temperature profile until the entire substrate has exited the vapor deposition apparatus.