Carbon nano-onions (CNOs) are a unique class of carbon nanomaterials, with a concentric fullerene-like structure and sp2-hybridized carbon atoms. Onions present high mechanical strength, good conductivity, the capability to intercalate alkali metals, showing promising applications in diverse fields, such as tribology, energy storage, and nanomedicine. Their production has been developed by several techniques, with the most interesting being the thermal annealing of carbon nanodiamonds because of the easy scalability (gram-scale) and morphologic control (size and shape form perfectly spherical to polygonal). However, this synthesis is commonly affected by the formation of strong aggregates larger than 100 nm, attributed to carbon soot formation or strong van der Waals interactions, hindering the work with small and individual particles, leading to an altered yield of functionalization. In this study we propose a method for CNO individualization based on strong acid treatment, yielding highly water dispersible nanoparticles. Analytical ultracentrifugation (AUC) analysis is employed as a technique to investigate the particle dimensions directly in dispersion, permitting an ensemble analysis free from further sample preparation bias. Moreover, we also provide a comprehensive evaluation of the common post-synthetic treatment methods, and their effects. By means of scanning transmission electron microscopy with medium angle annular dark field detector and electron energy loss spectroscopy (STEM-MAADF and EELS) we have shown images of individual CNOs. Their successful separation achieved in this study is significant for future research and applications in nanomedicine, electrochemistry, and materials composites, where sample homogeneity is critical.