The little coop inside the run is for broodies(mostly to break), grow-outs and meat birds. We decided it would work better for us to just keep it in there instead of removing it every time. To really clean it after each use, i do use bleach-soap & water, after that dries completely, it gets a very good spray down of homemade 'natural' spray. (lots of citrus oils/ spices/herbs + vinegars) We use sand to cover the bottom of the small coop run area & pull out tray. Makes clean up super easy, also keeps toes clean & dry.