An antifuse structure was analyzed using scanning electron microscope imaging and focused ion beam image slicing to generate a form of three-dimensional microscopy. This method reveals nanometer scale features that could not be easily imaged using a single focused ion beam cross-section. A novel end-point detection technique has been developed to control the thickness of the slice to about 2 nm. Voxel imaging and interpretive three-dimensional reconstruction was used to resolve volumes as small as 2 cubic nm3. It was determined that the fusing region for an antifuse is a complex mixture of material phases with an elliptical volume approximately 75 nm in diameter.