A cleaning system for cleaning a media transport device includes a cleaning substrate sized and configured to be inserted within at least a portion of a media travel pathway of a media transport device. The cleaning substrate comprises a cleaning face, along with a handle extending from the cleaning face. The handle is positioned to remain outside of the media transport device while the cleaning face is within the media transport device. The cleaning face comprises a plurality of cleaning elements, each of which is positioned to align with a belt, a drive roller, an idle roller, a drive roller/idle roller pair, or a sensor of the media transport device when the cleaning substrate within the media travel pathway. Methods of using a handled cleaning substrate are also disclosed.