The use of focused ion beam (FIB) systems is well established as a sample preparation and imaging tool in a wide range of applications, most notably, in the semiconductor and data storage industries, but also within material and biological sciences (Figs. 1-3). The real benefit of the FIB is that the same ion beam that is used for material removal and deposition is also used for imaging the sample, which results in highly precise and localized sample preparation. In addition, the FIB can be used to prepare samples through multiple layers with different material properties, and allows the rest of specimen to be kept intact for further analysis or processing. FIB is most commonly used to prepare samples for the transmission electron microscope (TEM), the scanning electron microscope (SEM), and for the FIB itself. The FIB, which is an imaging tool in its own right, can produce secondary-electron and -ion images and collect secondary ion mass spectrometry (SIMS) data.