Focused ion beam (FIB) tomography with combined electron backscatter diffraction (EBSD) and energy dispersive x-ray spectroscopy (EDS) is a technique capable of statistically characterizing the microstructure and spatial compositional variation of nuclear fuel in three-dimensions (3D). The 3D visualization from FIB tomography provides a comprehensive picture of the interconnected microstructural and compositional features that can impact fuel performance. While these features are often characterized with surface examination, the complexity and relationship of fission products and grain boundary networks may not fully be captured by these 2D methods. This work presents a practical guide to FIB tomography that is tailored to nuclear fuel characterization. The steps used to collect and process the data are provided along with the scripts used to process the data. Additionally, suggestions for future characterization efforts utilizing this approach are given.