A method is provided for preparing a prepatterned substrate for use in DSA integration. In one example, the method includes removing a radiation-sensitive material pattern overlying a patterned cross-linked polystyrene copolymer layer by a) exposure to a solvent vapor, b) exposure to a liquid solvent, and c) repeating steps a)-b) until the radiation-sensitive material pattern is completely removed. In another example, the method includes removing a neutral layer by affecting removal of an underlying patterned radiation-sensitive material layer, which includes swelling the neutral layer; and removing the radiation-sensitive material pattern and the swollen neutral layer in portions by exposing the swollen layer and pattern to a developer solution. Swelling the neutral layer includes a) exposure to a solvent vapor; b) exposure to a liquid solvent; and c) repeating steps a)-b) until the neutral layer is sufficiently swollen to allow penetration of the developing solution through the swollen neutral layer.