Understanding the chemical nature of the surface of carbon nanofibers (CNF) is critical in assessing their fundamental properties and tailoring them for the right application. To gain such knowledge, we present here a detailed X-ray adsorption spectroscopy (XAS) study accompanied by high resolution transmission electron microscopy (TEM) micrographs of two morphologically different CNF pairs (tetrahedral amorphous carbon (ta-C) grown “open structured” fibers and traditional bamboo-like “closed structured” fibers), where the surface chemical properties and structural features of the fibers are investigated in depth and the effects of nitric acid treatment on the fibers are revealed. The morphology of the fiber and/or the original seed- and adhesion layers markedly affect the response of the fibers to the acid treatment. Results also show that the nitric acid treatment increases the observed sp2 intensity and modifies the two types of fibers to become more-alike both structurally and with respect to their oxygen functionalities. The XAS and HRTEM results confirm that a short nitric acid treatment does not remove the Ni catalyst particle but, instead, oxidizes their surfaces, especially in the case of ta-C grown fibers.