Nanometer-scale organic surface structures have significant potential applications, e. g. in the field of nanoelectronics. Therefore the characterization but also the controlled production of these structures is of increasing importance. In recent years, it has been shown that scanning tunneling microscopy (STM) is, besides its wide use in the characterization of organic monolayers, also well suited for manipulation of these layers. In this study we investigate the possibility to use molecule corrals to confine the effects of manipulation of organic monolayers to small areas. Molecule corrals are nanometer-sized etch pits in the basal plane of highly ordered pyrolytic graphite (HOPG). They are formed by heating HOPG to 650° C in air. This technique produces corrals, which are uniformly circular and one monolayer deep. The radius is easily controlled by the etching time. Molecule corrals have previously been used to contain and study small numbers of molecules in their interiors and as highly controllable surface defects on graphite. We used a home build STM and a commercial STM (Multimode Nanoscope, Digital Instruments) for both, manipulation and characterization of self-organized organic monolayers on HOPG, with and without molecule corrals. Most of the experiments were performed under a liquid droplet of the organic compound in solution at room temperature. In this presentation, we will show, among others, results on diacetylene monolayers.