Modulation of oxide properties in a direction perpendicular to surfaces can be easily achieved by advanced thin film deposition tools. In contrast, simultaneous nanoscale modulation of properties in directions perpendicular and parallel to surfaces, as required for building three-dimensional (3D) nanometric devices, has remained elusive. Though bottom-up approaches allow obtaining controlled lateral growth, these techniques fail to achieve long-range order or do not allow simultaneous modulation of properties in the perpendicular direction. Here, we show that, by exploiting a dual strategy based on the spontaneous surface restructuration of some perovskite substrates and the layer-by-layer growth of nanometric heteroepitaxial perovskite layers, surfaces with laterally modulated surface relief, chemical termination, electrostatic potential, and electrical conductance can be obtained. As illustrative examples, conducting ferromagnetic manganite La 2/3Sr 1/3MnO 3 and ferroelectric BaTiO 3 ultrathin films have been grown on (001)SrTiO 3 and (001)(La 0.18Sr 0.82)(Al 0.59Ta 0.41)O 3 substrates with self-ordered chemical terminations. © 2012 American Chemical Society.