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Structured carbon nanomaterials (CNM) are class of the unique objects that combines advanced surface with chemical inertness, electrical conductivity and thermal stability, as well as the possibility of chemical modification and variation of pore size distribution. All these facts opens up huge prospects for their practical use in the manufacturing of electronic devices, systems for energy storage, generation and conversion, supports for metal catalysts and additives in composite materials, including polymeric. From the viewpoint of simplicity of hardware design and product yield among he possible methods of synthesis of such CNM as carbon nanotubes, nanofibers and structured carbon black, the most perspective is pyrolytic technique. It also allows to introduce heteroatoms such as B, N or P to the structures. For most of applications surface chemical modification is necessary. For the characterization of these materials at all stages of their synthesis, as a rule, thermogravimetry with mass spectral control of the degradation products, IR and Raman spectroscopy, as well as elemental analysis can be utilized. However, these methods do not allow evaluating localization of heteroatoms in the structure of the CNM or surface functional groups. Indispensable tool for this is high-resolution electron microscopy (HREM) and related techniques – electron diffraction (ED), electron energy loss spectroscopy (EELS) and electron probe microanalysis (EDS). The former can be used to identify the mechanisms of phase transformations in carbon structures, e.g. nanodiamonds to onion-like structures. Direct identification of light heteroatoms (mostly N and O) at CNM by EELS and, especially, EDS is hampered by low sensitivity and the destruction or displacement of the sample under high beam intensity. To do this, markers based on platinum or europium complexes were proposed. Much more effective is the use of thulium nitrate, which hydrolyzes in a significantly shorter period and forms more stable complexes with oxygen-containing ligands. For identification of hydrocarbon surface fragments iodine-containing compounds via chemical modification can be used. These elements are easily identified by EELS and EDS, the use of HAADF STEM mode makes their localization more clear. The results of experiments with unmodified CNM demonstrate the absence of signals from these markers.