The process of deuterium desorption from single-wall carbon nanotubes (SWNTs) modified by atomic (D) and molecular (D2) deuterium treatment was investigated in an ultrahigh vacuum environment using thermal desorption mass spectroscopy (TDMS). Microstructural and chemical analyses of SWNT material, modified by this deuterium interaction, were performed by means of a combination of scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). The results disclose characteristic features in the TDMS spectra of deuterium evolved from the SWNT material, which can be correlated to the microstructure of nanocarbon material modified by D-treatment. The TDMS spectra of deuterium originating from the large diameter rope type nanotube structures, resulting from a prolonged low-pressure (D + D2) gas mixture treatment, exhibit three overlapping desorption peaks: a dominant one with a desorption activation energy (Edes) of approx. 2.86 eV and lower intensity peaks at Edes of 1.50 and 2.46 eV. On the other hand, the TDMS spectra of deuterium taken from the “coral reef”-like carbon nanostructures, obtained after prolonged treatment of SWNTs to a high-pressure (D + D2) gas mixture produced at high temperature, reveal the coexistence of four superimposed desorption peaks with Edes ranging from 1.23 to 4.4 eV. A dominant desorption peak with Edes ≈ 4.4 eV, can be attributed to bulk diffusion of D trapped within this nanocapsule bulk structure.