Ultradense macroscopic arrays of ferromagnetic alloy nanowires exhibit unique properties that make them attractive both for basic physics studies and for prospective nanodevice applications in various areas. We report here on the production of self-organized equiatomic FePt nanowires produced by glancing-angle ion-beam codeposition on alumina nanoripple patterns at room temperature and subsequent annealing at 600 °C. This study demonstrates that periodically aligned FePt nanowires with tunable size (∼10-20 nm width and ∼0.5-10 nm height) can be successfully grown as a consequence of shadowing effects and low mobility of Fe and Pt on the rippled alumina surface. Moreover, the structure and magnetic properties of the FePt nanowires, which undergo a phase transition from a disordered A1 (soft) structure to a partially ordered L10 (hard) structure, can be modified upon annealing. We show that this behavior can be further exploited to change the effective uniaxial anisotropy of the system, which is determined by a strong interplay between the shape and magnetocrystalline anisotropies of the nanowires.