Uniform FePt nanoparticles were synthesized through nanostructuring of pulsed laser deposited FePt thin films by single shot H+ ion irradiation using a plasma focus device. The annealing temperature required for phase transition from low Ku face-centred cubic to high Ku face-centred tetragonal, for ion irradiated samples, is simultaneously lowered down to 400 °C. The energetic H+ ion irradiation significantly reduces the activation energy for atomic ordering by increasing the number of vacancies. The advantage of using a plasma focus device is that it can achieve nanostructuring in much shorter time, in single shot ion exposure with pulse duration of typically about a few hundreds of nanoseconds, as compared with much longer duration required by continuous ion sources.