This chapter gives an overview of the ordering of dyes on atomically flat conductive surfaces as revealed by scanning tunneling microscopy. Scanning tunneling microscopy provides detailed insight into the arrangement of dyes on various surfaces and unravels novel properties which arise as a result of the interaction of the dyes with the substrate. These high-resolution studies have been motivated by the importance of interfacial layers in view of material and device properties. Typical examples are provided of popular dye systems, including conjugated oligomers and polymers. In addition, the supramolecular ordering of mixtures of dyes and two-dimensional chirality is discussed. Scanning tunneling microscopy goes beyond imaging and its ability to manipulate dye molecules, both mechanically and chemically, is discussed. Finally, the use of scanning tunneling microscopy as a spectroscopy tool for probing the electronic properties of dye layers on surfaces is highlighted.