Methods and systems for deep learning alignment for semiconductor applications are provided. One method includes transforming first actual information for an alignment target on a specimen from either design data to a specimen image or a specimen image to design data by inputting the first actual information into a deep generative model such as a GAN. The method also includes aligning the transformed first actual information to second actual information for the alignment target, which has the same information type as the transformed first actual information. The method further includes determining an offset between the transformed first actual information and the second actual information based on results of the aligning and storing the determined offset as an align-to-design offset for use in a process performed on the specimen.