Metal impurities in the carbon nanotubes and carbon nanofibers play an important role in understanding their physical and chemical properties. We apply the Ni $K$-edge x-ray absorption fine structure analyses to the local electronic and geometric structures around embedded Ni impurities used as catalysts in a carbon nanofiber in combination with multiple scattering analyses. We find almost Ni catalysts as metal particles are removed by the purification treatment. Even after the purification, residual $100\phantom{\rule{0.3em}{0ex}}\mathrm{ppm}$ Ni species are still absorbed; most of them are in monomer structure with Ni-C bond length $1.83\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$, and each of them is substituted for a carbon atom in a graphene sheet.