A method of transferring one or more substrates between process modules or load lock stations while minimizing heat loss is provided. In some embodiments the method comprising the steps of: identifying a destination location D1 for a substrate S1 present at an initial processing location P1; if the destination location D1 is occupied with a substrate S2, maintaining the substrate S1 at the initial processing location P1; and if the destination location D1 is available, transferring the substrate S1 to the destination location D1. In accordance with additional embodiments, the method is carried out on a system for processing substrates which includes two or more process modules, a substrate handling robot, a load lock chamber, and a transverse substrate handler. The transverse substrate handler includes mobile transverse chambers configured to convey substrates to process modules, wherein each mobile transverse chamber is configured to maintain a specified gas condition during the conveyance of the substrates. The transverse substrate handler further includes a rail for supporting the mobile transverse chambers, wherein the rail is positioned adjacent to entry of the process modules, and drive systems for moving the mobile transverse chambers on the rail.