A method of operating a lithographic apparatus that comprises: a projection system configured to provide exposure radiation for patterning a substrate underneath the projection system; a first stage configured to support a first substrate; a second stage configured to support a second substrate; and a third stage accommodating a component that includes at least one of a sensor and a cleaning device; wherein the method comprises starting a pre-exposure scrum sweep operation after starting a substrate exchange operation; wherein during the pre-exposure scrum sweep operation, the third stage moves away from underneath the projection system while the second stage moves to underneath the projection system; wherein during the substrate exchange operation, the first substrate is unloaded from the first stage.