1. A method of non-destructive measurement of a depth of a feature in a structure, comprising: navigating and locating said feature using a scanning electron microscope (SEM) image; producing fluorescent emissions in said feature using the electron beam from said SEM; producing fluorescent emissions outside said feature using the electron beam from said SEM; counting, using an X-ray detector and a counting apparatus, said fluorescent emissions located such that emissions outside said feature travel through less structure than those inside said feature; and determining a depth of said feature based on a count of said fluorescent emissions made at inside and outside positions of said feature.