Methods of spatially directing the orientation and placement of multiple block copolymer (BCP) domains on isolated regions of a substrate are described. The methods involve epitaxially directing the assembly of BCP domains using spatial boundaries between regions with different surface composition, formed at the edges of isolated chemical regions on a background chemistry. Multiple vertical domains of BCP order on the isolated region, self-aligned in a direction parallel to edges of the isolated region. In some embodiments, vertical domains order on multiple isolated regions of a first chemistry of a chemical contrast pattern with horizontal domains on the regions of a second (background) chemistry of the chemical contrast pattern. Also provided herein are compositions resulting from the methods.