We report the growth and characterization of uniform-sized nanoparticles of cobalt on n-type silicon (100) substrates by swift heavy ion (SHI) irradiation. The Co thin films of 25-nm thicknesses were grown by e-beam evaporation and irradiated with two different types of ions, 45-MeV Li3+ and 100-MeV O7+ ions with fluences ranging from 1 × 1011 to 1 × 1013 ions/cm2. SHI irradiation, with the beam rastered over the area of the film, resulted in the restructuring of the film into a dense array of Co nanostructures. Surface topography studied by atomic force microscopy revealed narrowed size distributions, with particle sizes ranging from 20 to 50 nm, formed through a self-organized process. Ion fluence-dependent changes in crystallinity of the Co nanostructures were determined by glancing angle X-ray diffraction. Rutherford backscattering spectroscopy analysis showed the absence of beam-induced mixing in this system. Surface restructuring and beam-induced crystallization are the dominant effects, with the nanoparticle size and density being dependent on the ion fluence. Results are analyzed in the context of molecular dynamics calculations of electron-lattice energy transfer.