Surface processing of a rubrene single crystal immersed in ionic liquids is valuable for further development of low voltage transistors operated by an electric double layer. We performed a precise and clean surface processing based on the tip-induced dissolution of rubrene molecules at the ionic liquid/rubrene single crystal interfaces by using frequency modulation atomic force microscopy. Molecular resolution imaging revealed that the tip-induced dissolution proceeded via metastable low density states derived from the anisotropic intermolecular interactions within the crystal structure. © 2014 AIP Publishing LLC.