We report a versatile method for engineering arrays of nitrogen-vacancy (NV) color centers in diamond at the nanoscale. The defects were produced in parallel by ion implantation through 80 nm diameter apertures patterned using electron beam lithography in a polymethyl methacrylate (PMMA) layer deposited on a diamond surface. The implantation was performed with CN- molecules that increased the NV defect-formation yield. This method could enable the realization of a solid-state coupled-spin array and could be used for positioning an optically active NV center on a photonic microstructure.