Methods, systems and apparatus for swapping pods within a semiconductor processing tool during a substrate processing cycle. A dirty pod carrying a substrate in need of processing is provided within the processing tool, and the substrate is transferred into a processing chamber thereof. At least one clean pod is also provided within the processing tool. Upon substrate processing completion, the processed substrate is transferred from the chamber directly into a clean pod within the processing tool. Wherein a plurality of substrates are processed within the chamber, a plurality of clean pods may be provided within the tool whereby the plurality of substrates are transferred into a single clean pod or split into subsets that are transferred into different clean pods within the processing tool. The clean pod(s) carrying the processed substrate(s) are then transferred to other tool(s) for continued semiconductor fabrication processing.