Abstract: Methods and systems for deep learning alignment for semiconductor applications are provided. One method includes transforming design information for an alignment target on a specimen to a predicted image of the alignment target by inputting the design information into a deep learning model and aligning the predicted image to an image of the alignment target on the specimen generated by an imaging subsystem. The method also includes determining an offset between the predicted image and the image generated by the imaging subsystem 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 with the imaging subsystem.