A substrate protection and transport system and method for transitioning a substrate from atmospheric pressure to vacuum in a lithography tool. The system includes one or more removable substrate transport cassettes that support a substrate. The cassette can include a base portion and top portion, and can include a seal. Each cassette has at least one vent and at least one filter. The system further includes a box having a base and lid. The box holds one or more cassette-substrate arrangements. A storage rack having shelves for holding the box-cassette-substrate arrangement is also provided. Further, an entry-exit module having a loadlock is provided for transitioning the cassette-substrate arrangement from atmospheric pressure to vacuum. The entry-exit module can include a shuttle and/or elevator for transporting the cassette-substrate arrangement. During transitioning, the filter(s) and vent(s) restrict particles within the loadlock from entering the cassette-substrate arrangement and reaching a surface of the substrate.