A method of exposing a substrate (e.g. in a lithographic apparatus comprising a substrate table to support a substrate) according to one embodiment of the invention includes performing first and a second height measurement of a part of at least one substrate with a first and second sensor, generating and storing an offset error map based on a difference between the measurements; generating and storing a height map of portions of the substrate (or another substrate that has had a similar processing as the part) by performing height measurements with the first sensor and correcting this height map by means of the offset error map; and exposing the substrate (or the other substrate).