An inline transfer system and method are provided for the secure transport and efficient processing of substrates such as glass substrates or semiconductor devices. A rotary conveyor is provided that includes a plurality of air nozzles which inject air to move a substrate above the plurality of air nozzles without the plurality of air nozzles making contact with the substrate. At least two independent processing units are operably coupled to the rotary conveyor. Advantageously, because a plurality of substrates may be processed in parallel, greater efficiency and flexibility are provided. Because the substrate can be moved without physical contact between the structure of the air nozzles and the substrate, the transfer is secure, clean, and efficient.