Core/shell CuAg and alloyed CoPt have been synthesized using two vapor phase deposition techniques. For CuAg prepared by Thermal Evaporation (TE), the size and the morphology of the Cu cores are the key parameters to promote the formation of the core/shell arrangement. For CoPt synthesized by Pulsed Laser Deposition (PLD), the growth kinetics of nanoparticles, depending on the deposition rate, the substrate nature and the temperature, controls the nanoparticle morphology. The competition between the growth and the ordering kinetics governs the nanoparticle structure. By reducing the growth kinetics, as-grown L1(0) ordered nanoparticles are obtained according to the bulk phase diagram.