The observation of morphological details down to the nanometer range of the outer surface of micro-, submicro- and nanoparticles in a high-resolution scanning electron microscope (SEM) was extended with in-depth observation by enabling the transmission mode in the SEM, i.e. TSEM. The micro- and nanocapsules characterized in this study were fabricated as depots for protective agents to be embedded in innovative self-healing coatings. By combining the two imaging modes (upper and in-depth observation) complementing each other a better characterisation by a more comprehensive interpretation of the "consistency" of the challenging specimens, e.g. including details "hidden" beyond the surface or the real specimen shape at all, has been attained. Furthermore, the preparation of the quasi electron transparent samples onto thin supporting foils enables also elemental imaging by energy dispersive X-ray spectroscopy (EDX) with high spatial resolution. Valuable information on the elemental distribution in individual micro-, submicro- and even nanocapsules completes the "3D" high resolution morphological characterization at the same multimodal SEM/TSEM/EDX system.