The influence of experimental condition on morphology of FePt and Sm-Co nanoparticles synthesized by sputtering in a relatively high gas pressure has been studied. The sputtering apparatus is equipped with an annealing furnace that enables pre-deposition annealing of the nanoparticles. The effect of the annealing temperature on the ordering to the L10 FePt nanoparticles was also investigated. The morphology of the particles depends on a gas pressure and gas flow rate, but the sensitivity to experimental condition differs between FePt and Sm-Co. The morphology and domain structure of FePt nanoparticle are relatively the same in a wide range of experimental condition, whereas those of Sm-Co nanoparticle are significantly changed by variation of a gas pressure. FePt nanoparticles annealed in the annealing furnace prior to their deposition onto the substrate have the ordered L10 phase, which has an advantage for producing a magnetic recording media.