A method includes: providing a substrate having a plurality of chemically contrasted alignment features, and depositing a self-assembled material on at least a portion of the substrate, wherein the position and/or orientation of substantially spherical or cylindrical domains of the self-assembled material is directed by the alignment features, to form a nanostructure pattern, and wherein the period of the alignment features is between about 2 times and about 10 times the period of the spherical or cylindrical domains. An apparatus fabricated according to the method is also provided.