A system and method are used to compensate for distortions or aberrations in an image formed in a projection system. Pattern data is generated corresponding to features to be formed on a substrate. At least one of aberrations and distortions of a projection optical system are measured. The pattern data is altered based on the measuring step. The altered pattern data is transmitted to a patterning device to control individually controllable elements coupled to the patterning device. Non uniformities in one or both of a field and pupil of an illumination system can also be measured and used to alter the pattern data.