Graphoepitaxy directed self-assembly methods generally include grafting a conformal layer of a polymer brush onto a topographic substrate. A planarization material, which functions as a sacrificial material is coated onto the topographic substrate. The planarization material is etched back to a top surface of the topographic substrate, wherein the etch back removes the polymer brush from the top surfaces of the topographic substrate. The remaining portion of the polymer brush is protected by the remaining planarization material below the top surface of the topographic substrate, which can be removed with a solvent to provide the topographic substrate with a conformal polymer brush below the top surface of the topographic substrate. The substrate is then coated with a block copolymer and annealed to direct self-assembly of the block copolymer. The methods mitigate island and/or hole defect formation.