A study was conducted to demonstrate a methodology that was used for tuning the crystal structure and magnetic properties of iron platinum (FePt) binary nanomagnets. Tuning of the crystal structure of nanoparticles involved both thermodynamic and kinetic factors. The binary phase diagram of equiatomic FePt alloy showed that it had two solid-state phases, such as disordered and fct ordered phase, with fcc as the high-temperatured stable phase. Post-deposition annealing process was used to get the ordered phase. The annealing process was a first-order phase transformation process, which required nucleation sites for the ordering to originate. It was also observed that grain boundaries and crystal defects in FePt thin films can supply supply the starting points for phase transformation. The technique used for tuning the crystal structure of FePt binary alloy was also applied to other nanometer-scale materials preparation for structure and property control.