Affymetrix of Santa Clara, Calif., has received US Patent No. 6,789,040, “System, method, and computer software product for specifying a scanning area of a substrate.” Systems, methods, and computer program products are described for specifying a scanning area of a substrate. In accordance with one method, steps include receiving location data corresponding to a plurality of probe-feature locations on the substrate, storing the location data, accessing the location data, and scanning the substrate based on the accessed location data.