Methods of directing the self assembly of block copolymers on chemically patterned surfaces to pattern discrete or isolated features needed for applications including patterning integrated circuit layouts are described. According to various embodiments, these features include lines, t-junctions, bends, spots and jogs. In certain embodiments a uniform field surrounds the discrete feature or features. In certain embodiments, a layer contains two or more distinct regions, the regions differing in one or more of type of feature, size, and/or pitch. An example is an isolated spot at one area of the substrate, and a t-junction at another area of the substrate. These features or regions of features may be separated by unpatterned or uniform fields, or may be adjacent to one another. Applications include masks for nanoscale pattern transfer as well as the fabrication of integrated circuit device structures.