Dip-Pen Nanolithography (DPN) is a scanning-probe lithography technique that permits the chemical functionalization of surfaces with nanoscale precision. We describe the use of DPN to pattern a variety of soft organic and biological nanostructures that we use to direct the assembly of materials processed from solution. For example, by selectively functionalizing electrodes with nanoscale DNA patterns we are able to capture specific sizes of metal nanoparticles and measure their electrical properties. In another application, by generating high-resolution (sub-100 nm) patterns with different functional self-assembled monolayers on various electrode surfaces, we have the ability to systematically nucleate, as well as guide, the phase separation behavior of polymer films when they are spin-coated onto substrates. We discuss the potential use of these techniques in applications ranging from biological diagnostics to organic electronics.