1. A method for determining a position of output of an inspection system in a design data space, comprising: 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; storing information for the single feature without the design data for the features that are merged, wherein the information comprises a position of the single feature in a design data space; aligning output of an inspection system for the wafer to the information for the single feature; determining a position of a first portion of the output aligned to the single feature in the design data space based on the position of the single feature in the design data space; and determining positions in the design data space of other portions of the output based on the position of the first portion of the output in the design data space, wherein the merging step, the storing step, the aligning step, determining the position of the first portion, and determining the positions of the other portions are performed by one or more computer systems.