1. A method for correcting a pattern placement on a substrate, the method comprising: detecting three reference points for a substrate; detecting a plurality of sets of three die location points, each set indicative of an orientation of a die, the plurality of sets include a first set associated with a first die and a second set associated with a second die; calculating a local transformation for an orientation of the first die and the second die on the substrate; selecting three orientation points from the plurality of sets of three die location points wherein the orientation points are not members of the same set; calculating a first global transformation of the substrate from the selected three points from the set of points; and storing the first global transformation and the local transformation for the substrate.