Traditionally, focused ion beam (FIB) microscopy systems have been used as instruments to repair integrated circuits, isolate defects or prepare mateiials for characterization with other techniques. Recently however, FIB microscopy has been used extensively as a standalone characterization technique. Typically, FIB microscopy can be used to probe site specific areas of a sample through secondary electron and ion imaging, energy dispersive x-ray analysis (EDX), or secondary ion mass spectroscopy (SIMS). These analyses will often combine two-dimensional elemental mapping or sputter depth profiles with imaging to investigate spatial variations of chemical and imaging signals. Inherently, these investigations are confined to two dimensions but often, complex materials problems are more easily understood if chemical and geometric information can be collected.