Nanoscale structural features of a novel self-assembling DNA based nanostructure have been resolved. Image data is of sufficient resolution to allow molecular orientation and the effect of surface adsorption to be characterized. This has been achieved using AFM with probes employing carbon nanotubes attached via a thin film of plasma polymerized hexane. This presents the nanotube with a highly hydrophobic coating to which it can adsorb, increasing production success and probe robustness.