The three-dimensional ultra-structure is the comprehensive structure that cannot be observed from a two-dimensional electron micrograph. Array tomography is one method for three-dimensional electron microscopy. In this method, to obtain consecutive cross sections of tissue, connected consecutive sections of a resin block are mounted on a flat substrate, and these are observed with scanning electron microscopy. Although array tomography requires some bothersome manual procedures to prepare specimens, a recent study has introduced some techniques to ease specimen preparation. In addition, array tomography has some advantages compared with other three-dimensional electron microscopy techniques. For example, sections on the substrate are stored semi-eternally, so they can be observed at different magnifications. Furthermore, various staining methods, including post-embedding immunocytochemistry, can be adopted. In the present review, the preparation of specimens for array tomography, including ribbon collection and the staining method, and the adaptability for correlative light and electron microscopy are discussed.