Abstract: Methods and systems for determining a position of output generated by an inspection subsystem in design data space are provided. One method includes selecting one or more alignment targets from a design for a specimen. At least a portion of the one or more alignment targets include built in targets included in the design for a purpose other than alignment of inspection results to design data space. At least the portion of the one or more alignment targets does not include one or more individual device features. One or more images for the alignment target(s) and output generated by the inspection subsystem at the position(s) of the alignment target(s) may then be used to determine design data space positions of other output generated by the inspection subsystem in a variety of ways described herein.