Nearly equi-atomic FePt films were deposited on a silicon substrate with a native SiO2 layer by co-sputtering technique. Structural and magnetic properties of the films are influenced by the growth temperature. The native SiO2 layer acts as a diffusion barrier for the FePt film on Si. In the absence of diffusion of Fe and Pt with Si substrate, a high coercivity (∼8.2 kOe) L10 Fe50Pt50 phase is formed. Depending on the growth temperature and the thickness/quality (continuously or containing some pinholes) of SiO2 layer, diffusion of FePt film with Si substrate is observed. Diffusion results in the change in film composition, and formation of various Fe- and Pt-silicide phases along with the flower-like surface morphology. Growth of flower like nano-structures are shown to be governed by the accelerated diffusion of Fe on a dimpled surface of Si substrate. The detailed structural and magnetic characterization revealed that the flower-like patterns are composed of chemically ordered antiferromagnetic FePt3 phase (Q2-type). The Neel's temperature for these flowers-like nano-structures is ∼80 K and they are surrounded by a ferromagnetic matrix. Growth mechanism of flower-like patterns is identified. Site specific growth of antiferromagnetic nano-structures in a ferromagnetic matrix is also demonstrated.