Dispersion of carbon nanofibers subjected to post production processing, heat treatment (HT) and pyrolytical stripping (PS), is investigated in aqueous suspension using small-angle light scattering. Both samples exhibit a hierarchical morphology consisting of small-scale aggregates and large-scale fractal agglomerates that precipitate rapidly. Although small-scale objects are formed by side-by-side aggregation of the nanofibers in both cases, the determination of the size distribution by assuming a tube model indicates that the PS sample is much less aggregated because of the presence of chemical vapor deposition layer. For HT fibers, the size of large agglomerates remains nearly unchanged during the precipitation process. For PS fibers, large agglomerates precipitate with time, leaving small entities in suspension, which never agglomerate. The HT nanofibers show greater degree of aggregation and agglomeration due to their highly ordered graphite nature. The carbon nanofiber structure significantly influences the dispersion of carbon nanofibers. These findings have significant implications for potential applications of carbon nanofibers in the fields of nanocomposites and biomedical nanostructures.