To prevent a substrate from expanding significantly to generate overlay errors an exposure operation takes place in two parts. A first part exposes boundary areas and a second part exposes the larger, bulk areas. In one example, a portion of the substrate is fixed and the substrate is exposed progressively from parts furthest from the fixed portions towards the fixed portion. In another example, a plurality of high velocity scans take place instead of a single slow scan, and the substrate is allowed to cool between the high velocity scans. In another example, a lithographic apparatus is heated in order to maintain a temperature differential between the apparatus and the surrounding environment, and to minimize any fluctuation due to the exposing radiation.