Carbon nanofibers were oxidized in air at 350 °C under the influence of a 3 MeV electron beam at doses of 1000 and 3500 kGy. XPS analysis showed that oxygen was readily incorporated on the surface: the ratio O 1s/C 1s increased approximately by a factor of three when the carbon nanofibers were irradiated at 3500 kGy. The oxidized nanofibers exhibited better dispersion than as-received nanofibers when mixed with water/methanol (50% v/v). Raman spectroscopy revealed that the ID/IG ratios were statistically unchanged for all samples because the damage on the nanofiber surface was highly localized and did not lead to modifications on the bulk carbon nanofiber structure. On the other hand, SEM, TEM, and AFM images illustrated that cutting, welding, and collapse may occur on the structure of irradiated nanofibers. BET analysis showed that the surface area of irradiated samples did not significantly increase, probably because the radiation process may lead to micro-porosity formation. The temperature during irradiation had no effect on the nanofibers’ surface and the thermal stability of the irradiated samples was determined to be lower.