A lithographic apparatus is used to manufacture a plurality of devices on a substrate. A height map is obtained representing a topographical variation across the substrate. Using the height map the apparatus controls imaging of a field pattern at multiple field locations across the substrate. The field pattern includes a plurality of individual device areas. For field locations near the substrate's edge, the height map data is used selectively so as to ignore topographical variations in one or more individual device areas. Whether a device area is to be ignored is determined at least partly based on the height map data obtained for the current exposure. Alternatively or in addition, the selection can be based on measurements made at the corresponding device area and field location on one or more prior substrates, and/or on the same substrate in a previous layer.