Methods, systems, and apparatus, including medium-encoded computer program products, for computer aided repair of physical structures include: generating a two dimensional difference image from a first three dimensional model of at least one actual three dimensional surface of a manufactured object, and a second three dimensional model of at least one source three dimensional surface used as input to a manufacturing process that generated the manufactured object; obtaining from an image-to-image translation based machine learning algorithm, trained using pairs of input images representing deformed and deformed plus surface defected added versions of a nominal three dimensional surface, a translated version of the two dimensional image; generating from the translated version of the two dimensional image a third three dimensional model of at least one morphed three dimensional surface corresponding to the at least one source three dimensional surface. Further, defects can be removed based on the third three dimensional model.