Abstract: A new method is provided to align overlying layers for wafer stepper tools that are use for the manufacturing of semiconductor devices. A reference stepper and a reference mask are used, the mask contains a pattern of reference alignment marks that are created using this mask in a reference first surface on a substrate. A matching stepper that must be calibrated against the reference stepper is then used to create, using the reference mask, alignment marks in a second surface on a substrate. The alignment error between the reference alignment marks and the alignment marks that have been created in the second surface are measured and used as input to software modeling programs that provide numerical data indicating the corrections that must be applied to the matching stepper in order to adjust the alignment of the matching stepper to the alignment of the reference stepper.