Methods are provided that, in some embodiments that provide alignment of a first layer of a printing plate on a chuck. For example, in one embodiment, images of reference marks on a chuck are captured to determine the initial positions of the reference marks on the chuck. A reference model is created from those initial positions. Images of alignment marks on a reference plate are captured and the locations of the alignment marks are determined. A reference plate model is created from the positions of the alignment marks. A mapping model is then created from the reference model and the reference plate model.