A method for coating substrates with multiple coating layers can comprise: establishing a sub-atmospheric pressure within a coating system; transferring each substrate from outside the coating system to inside the coating system though a transfer lock; heating each substrate in a heating zone before entering a coating zone; traversing the coating zone in a first direction of movement and applying a first coating layer to each substrate in the coating zone using expanding thermal plasma type of plasma enhanced chemical vapor deposition; traversing the coating zone a second time and applying a second coating layer to each substrate in the coating zone using expanding thermal plasma type of plasma enhanced chemical vapor deposition; determining if the coating zone is occupied or vacant; if the coating zone is vacant, purging a heater zone module with inert gas; and pumping the inert gas out of the coating zone through ports located in the coating zone.