A lithographic apparatus includes a patterning subsystem for transferring a pattern from a patterning device onto a substrate controlled in accordance with recorded measurements of level variations across a surface of the substrate. A level sensor is provided for projecting a level sensing beam of radiation to reflect from a location on the substrate surface and for detecting the reflected sensing beam to record the surface level at said location. The level sensor incorporates at least one moving optical element to scan the substrate surface by optical movement in at least one dimension to obtain measurements of surface level at different locations without mechanical movement between the level sensor and the substrate. Optical path length equalization measures may be employed, using shaped reflectors and/or additional moving mirrors, to avoid focus variation during the scan.