In this study, advanced control of crystallographic orientations and magnetic properties of self-assembled nanostructures via rational selections of substrates is demonstrated. We show that in the perovskite-spinel BiFeO(3)-CoFe(2)O(4) model system the crystal orientation of self-assembled CoFe(2)O(4) nanopillars can be tuned among (001), (011), and (111), while that of the BiFeO(3) matrix is fixed in (001). Moreover, the resultant CoFe(2)O(4) nanopillars appear in various shapes: pyramid, roof, and triangular platform, respectively. The tunable nanostructures through this approach enable the control of material functionality such as the magnetic anisotropy of CoFe(2)O(4). This study opens a new pathway for the engineering of self-assembled heteroepitaxial nanostructures.