The present application discloses methods and systems for calibrating a scanning system. The scanning system comprises a light-transmissive platen defining a top surface and a bottom surface, a controller, a document handler, and a scanner bar for recording image data from documents at various document heights. In one embodiment, the calibration method proposes the use of two calibration strips in a document scanning system that has both platen scanning and Constant Velocity Transport (CVT) scanning modes. In another embodiment, a scanner is disclosed with a dual calibration target or a single calibration target that is manufactured with two (2) different heights to correct the illumination profile at the CVT scanning height or at the platen scanning height.