The design of artificial vortex pinning landscapes is a major goal towards large scale applications of cuprate superconductors. While disordered nanometric inclusions have shown to modify their vortex phase diagram and to produce enhancements of the critical current1,2, the effect of ordered oxide nanostructures remains essentially unexplored. This is due to the very small nanostructure size imposed by the short coherence length, and to the technological difficulties in the nanofabrication process. Yet, the novel phenomena occurring at oxide interfaces open a wide spectrum of technological opportunities to interplay with the superconductivity in cuprates. Here we show that the unusual long range suppression of the superconductivity occurring at the interface between manganites and cuprates affects vortex nucleation and provides a novel vortex pinning mechanism. In particular, we show evidence of commensurate pinning in YBCO films with ordered arrays of LCMO ferromagnetic nanodots. Vortex pinning results from the proximity induced reduction of the condensation energy at the vicinity of the magnetic nanodots, and yields an enhanced friction between the nanodot array and the moving vortex lattice in the liquid phase. This result shows that all-oxide ordered nanostructures constitute a powerful, new route for the artificial manipulation of vortex matter in cuprates.