A method for controlling a scanning exposure apparatus configured for scanning an illumination profile over a substrate to form functional areas thereon. The method includes determining a control profile for dynamic control of the illumination profile during exposure of an exposure field including the functional areas, in a scanning exposure operation; and optimizing a quality of exposure of one or more individual functional areas. The optimizing may include a) extending the control profile beyond the extent of the exposure field in the scanning direction; and/or b) applying a deconvolution scheme to the control profile, wherein the structure of the deconvolution scheme is based on a dimension of the illumination profile in the scanning direction.