We demonstrate an advanced fabrication method for perfectly position-controlled ferromagnetic semiconductor (Fe,Zn)(3)O(4) nanodot arrays down to several hundred nanometers in size surrounded by a ferroelectric BiFeO(3) matrix. By performing position-selective crystal growth of perovskite BiFeO(3) on the position-controlled epitaxial spinel (Fe,Zn)(3)O(4) nanodot-seeding template, which is prepared using a hollow molybdenum mask lift-off nanoimprint lithography process on a perovskite La-doped SrTiO(3)(001) substrate, we produce functional oxide three-dimensional lateral heterojunctions. The position-selectivity can be explained based on standard surface diffusion theory with a critical nucleation point. Establishing this fabrication process could lead to innovative nanointegration techniques for spintronic oxide materials.