In the search for the integration of carbon nanostructures in composite and functional materials, covalent organic reactions are successfully performed. This approach resulted in the construction of tailored chemical interfaces facilitating incorporation of nanocarbons. By a combination of different characterization techniques, such as high-resolution X-ray photo-spectroscopy, thermogravimetric analysis, Raman spectroscopy, UV-vis-nIR, and fluorescence spectroscopies, it is possible to identify and quantify the functional moieties covalently attached to the carbon frame. However, the determination of the structural conformation of functionalized nanostructures remains a difficult task. In this work, we present a straightforward methodology to visualize by transmission electron microscopy the functional moieties covalently attached to the carbon network in carbon nanotubes and graphene. The identification of the functionalities occurs in colloidal dispersions by using gold nanoparticles (AuNPs) as discriminating markers by molecular recognition or by the direct growth of AuNPs on the oxygenated moieties. This methodology, in combination with other characterization analysis, is expected to improve the design of hierarchical interfaces by the spatial localization of the functionalities responsible for colloidal stabilization in solvents with different polarities, different from their homogeneous incorporation into different matrices.