Systems and methods for determining a position of output of an inspection system in design data space are provided. One method includes merging more than one feature in design data for a wafer into a single feature that has a periphery that encompasses all of the features that are merged. The method also includes storing information for the single feature without the design data for the features that are merged. The information includes a position of the single feature in design data space. The method further includes aligning output of an inspection system for the wafer to the information for the single feature such that positions of the output in the design data space can be determined based on the position of the single feature in the design data space.