1. A method of measuring a relationship between features in two different images of a work piece, the images produced by a charged particle beam system, comprising: directing a charged particle beam toward a work piece; detecting first emissions from the work piece in response to the charged particle beam to produce a first image; detecting second emissions from the work piece in response to the charged particle beam or to a second charged particle beam to produce a second image; automatically locating a first feature in the first image; automatically locating a second feature in a second image; and measuring a spatial relationship between the first feature and the second feature using spatial information from the second feature.