Methods and apparatus for imaging a structure and a related processor-readable medium are disclosed. A surface of a substrate (or a portion thereof) is exposed to a gas composition. The gas composition includes one or more components that etch the substrate upon activation by interaction with a beam of electrons. A beam of electrons is directed to one or more portions of the surface of the substrate that are exposed to the gas composition to etch the one or more portions. A plurality of images is obtained of the one or more portions at different instances of time as the one or more portions are etched. A three-dimensional model of one or more structures embedded within the one or more portions of the substrate is generated from the plurality of images.