A method and system for positioning a wafer on a bake plate in a processing module that includes lowering a bake plate cover assembly over the wafer during a baking process, raising the bake plate cover assembly after the baking process, removing the wafer, determining whether the bake plate cover assembly requires cleaning, then either processing another wafer if the cover assembly does not need cleaning or establishing a cleaning process for the bake plate cover assembly if the cover does need cleaning. Automated sensing of the state of the cover assembly may be employed, and cleaning process may be automatically performed in response to the cleaning need determination.