We used a combination of dip-pen nanolithography and scanning optical confocal microscopy to fabricate and visualize luminescent nanoscale patterns of various materials on glass substrates. We show that this method can be used successfully to push the limits of dip-pen nanolithography down to controlled deposition of single molecules. We also demonstrate that this method is able to create and visualize protein patterns on surfaces. Finally, we show that our method can be used to fabricate polymer nanowires of controlled size using conductive polymers. We also discuss the factors that influence the size of these nanowires.