Spinning is a phenomenon not only present in spiders, but also in many other arthropods. The functional morphology and complexity of spinning organs is often poorly understood. Their elements are minute and studying them poses substantial methodological difficulties. This study presents a three-dimensional reconstruction of a silk gland of Embia sp. on cellular level, based on serial sections acquired with serial block-face scanning electron microscopy (SBFSEM) to showcase the power of this method. Previous studies achieved either high resolution to elucidate the ultrastructure or satisfying three-dimensional representations. The high-resolution achieved by SBFSEM can be easily used to reconstruct the three-dimensional ultrastructural organization of cellular structures. The herein investigated spinning apparatus of Embioptera can be taken as an example demonstrating the potential of this method. It was possible to reconstruct a multinucleated silk gland containing 63 nuclei. We focused on the applicability of this method in the field of morphological research and provide a step-by-step guide to the methodology. This will help in applying the method to other arthropod taxa and will help significantly in adapting the method to other animals, animal parts and tissues.