TEM除了具有優越的二維影像分辨率外，也有三維的成像能力，可進一步探索材料的三度空間顯微結構。TEM立體影像顯微術屬於較簡單的三維立體成像術，可分析簡單的晶體缺陷結構，如差排、疊差，和一些具有特定晶面的析出物等。電子束體層攝影術則是較複雜的技術，包含影像攝取、調整、重建與具像化四步驟，此技術可分析包括半導體元件等複雜的顯微結構。

Besides high resolution for 2D images, TEM also offers 3D imaging ability which is able to explore 3D microstructure in the materials. TEM stereo microscopy can resolve simple crystal defect structure such as dislocations, stacking faults, and some precipitates with defined crystal planes; while TEM tomography is a more complicated technique, which including acquisition, alignment, reconstruction, and visualization for steps, being applied to explore more complicated microstructure including the architectures of semiconductor devices.