An atmospheric plasma processing system is presented. In accordance with embodiments of the present invention, an atmospheric pressure plasma microwave processing apparatus includes a processing area or chamber wherein parts are processed; at least one multi-mode microwave reactor coupled to receive parts for processing; at least one magnetron coupled to at least one multi-mode microwave reactor to provide microwave energy; and a delivery system coupled to at least one multi-mode microwave reactor to deliver the parts into and out of at least one reactor, wherein a plasma can be generated at atmospheric pressure and provided to the parts in at least one multi-mode microwave reactor.