With the rapid evolvement in the automation of serial micrographs, acquiring fast and reliably giga- to terabytes of data is becoming increasingly common. Optical, or physical sectioning, and subsequent imaging of biological tissue at high resolution, offers the chance to postprocess, segment, and reconstruct micro- and nanoscopical structures, and then reveal spatial arrangements previously inaccessible or hardly imaginable with simple, single section, two-dimensional images. In some cases, three-dimensional models highlighted peculiar morphologies in a way that two-dimensional representations cannot be considered representative of that particular object morphology anymore, like mitochondria for instance. Observations like these are taking scientists toward a more common use of 3D models to formulate functional hypothesis, based on morphology. Because such models are so rich in details, we developed tools allowing for performing qualitative, visual assessments, as well as quantification directly in 3D. In this chapter we will revise our working pipeline and show a step-by-step guide to analyze our dataset.