A method includes providing a layered structure on a substrate, the layered structure including a bottom layer formed over the substrate and a photoresist layer formed over the bottom layer, exposing the photoresist layer to a radiation source, developing the photoresist layer, patterning the bottom layer and removing portions of the substrate through openings in the patterned bottom layer. In some embodiments, a middle layer is provided between the bottom layer and the photoresist layer. The material of the bottom layer includes at least one cross-linking agent that has been functionalized to decrease its affinity to other materials in the bottom layer.