The structural properties of ionic liquid/rubrene single-crystal interfaces were investigated using frequency modulation atomic force microscopy. The spontaneous dissolution of rubrene molecules into the ionic liquid was triggered by surface defects such as an oxidized rubrene or a vacancy, leading to the formation of a clean interface irrespective of the initial conditions. Force curve measurements revealed that a few solvation layers of ionic liquid molecules formed at the interface. We have also measured electric characteristics of electric double layer field-effect transistor based on the ionic liquid/rubrene single crystal interfaces. In contrast to usual devices, the mobility of field induced career was found to gradually increase with time for a day, consistent with the time scale of the spontaneous dissolution. These specific properties are discussed with respect to the microscopic understanding of electric double-layer transistors.