Chemically ordered FePt binary alloys with L10 face-centered tetragonal (fct) structure have recently attracted considerable attention due to their excellent intrinsic magnetic chemical and mechanical properties. In particular, one-dimensional (1-D) arrays of FePt alloys are prospective materials for ultrahigh density magnetic storage media. We describe a new method to fabricate FePt alloy nanostructures embedded in the nanochannels of anodic alumina templates (AAT) and SBA15 silica through infiltrating porous membranes with FePt nanoparticles. SBA15 silica nanotube is a honeycomb structure with tubular channels of 9 nm in diameter, extending through long particles. In contrast AAT have morphology of a membrane with regular array of pores 60 nm in diameter. To transform the FePt alloy phase from chemically disordered face-centered-cubic to chemically ordered L10 phase the membrane was annealed at in a H2–N2 gas mixture for 2 h. Transmission electron microscope (TEM) and field emission scanning electron microscope (FESEM) show that nanoparticles transformed into isolated superparamagnetic nanoparticles in SBA15 and elongated nanostructure in AAT due to the annealing treatment. The magnetization was measured by quantum interference device (SQUID). The ordered fct FePt polycrystalline nanostructure in AAT have high magnetic anisotropy and thus large coercivity up to 1.1 T at room temperature.