1. A method for generating golden template images in a vision system to inspect an acquired runtime image of an object with a multi-layer printed pattern comprising the steps of: performing a registration process on runtime images using registration models each trained on respective canonical layer masks, and outputting poses; based upon the poses, generating warped layer masks; computing combination masks based upon differing combinations of the warped layer masks; estimating intensity of regions for the combination masks; and blending the estimated intensity values associated with the combination masks to generate a golden template image.