Embodiments provided herein provide methods for preparing patterned neutral layers using photolithography, and structures prepared using the same. A method of preparing a structure may include disposing a film over a surface of a substrate, and removing plurality of elongated trenches from the film so as to define a plurality of spaced lines. A neutral layer may be disposed over the outer surface of each line, and may include a neutral group attached to the outer surface of that line via a covalent bond or a hydrogen bond. The surface of the substrate between the lines may be substantially free of the neutral layer.