Over the years, FIB-SEM tomography has become an extremely important technique for the three-dimensional reconstruction of microscopic structures with nanometric resolution. This paper describes in detail the steps required to perform this analysis, from the experimental setup to the data analysis and final reconstruction. To demonstrate the versatility of the technique, a comprehensive list of applications is also summarized, ranging from batteries to shale rocks and even some types of soft materials. Moreover, the continuous technological development, such as the introduction of the latest models of plasma and cryo-FIB, can open the way towards the analysis with this technique of a large class of soft materials, while the introduction of new machine learning and deep learning systems will not only improve the resolution and the quality of the final data, but also expand the degree of automation and efficiency in the dataset handling. These future developments, combined with a technique that is already reliable and widely used in various fields of research, are certain to become a routine tool in electron microscopy and material characterization.