A device manufacturing method in a lithographic apparatus includes determining a plurality of positions on a substrate. The plurality of positions on a measurement substrate are scanned in a first direction to determine a first substrate map of the substrate levels of the measurement substrate. The plurality of positions on the measurement substrate are scanned in a second direction to determine a second substrate map of the substrate levels of the measurement substrate. A difference map is produced that includes information of the difference in measurement substrate surface level using the first substrate map and the second substrate map.