We report a first study on the use of chemically nanopatterned substrates to induce long-range ordering (in the plane of the film) of perpendicular cylinders confined between the substrate and an upper homogeneous surface. Two conditions are essential for obtaining the long-range ordering: a lower hexagonally patterned substrate, commensurate with perpendicular cylinders having the same dimensions and packing as in the bulk, and an upper neutral or weakly preferential surface for the longer blocks. By examining the spatial fluctuations of perpendicular cylinders, we propose that combining nanopatterned substrates with electric fields perpendicular to the film could reach the ultimate goal of producing long-range ordered perpendicular cylinders as templates for nanolithography.