In one method of compensating for the distortion of front-to-backside alignment optics, a displacement vector between the estimated position of a substrate mark and the actual position of a substrate mark is calculated. An optical correction array is also calculated by moving a reference substrate by a fixed amount and comparing how far an image of a point on the back side of a reference substrate moves to how far a corresponding point on the front side of the substrate moves. The displacement vector and optical correction array may then be used to accurately calculate the position of further substrates.