Realizing surface wettability tuning at the submicron-scale resolution is expected to enable the fabrication of micro/nano-structured fluidic devices and is particularly important in nanobiotechnology and high-resolution printing. Herein, we propose an approach to modify the wettability of self-assembled monolayer surfaces using focused ion beam (FIB) irradiation. The contact angle of the irradiated region changed from hydrophobic to hydrophilic by increasing the ion dosage. The chemical composition and associated depth profile of the sample surfaces were analyzed by glow discharge-optical emission spectroscopy. The results indicated that the content of fluorine at the surface decreased after FIB irradiation of the samples. A submicron-scale hydrophobic-hydrophilic hybrid surface was then fabricated by forming hydrophilic dots with diameters of similar to 110 nm on a hydrophobic surface by FIB irradiation. The difference in wettability of the hydrophobic and hydrophilic areas on the surface was confirmed by microscale condensation and evaporation experiments. Condensed droplets with diameters of similar to 300 nm appeared on the surface according to the fabricated pattern, thus suggesting that condensation preferentially occurred on the hydrophilic dots than on the hydrophobic surface. Furthermore, tiny droplets remained on the hydrophilic dots following evaporation of the larger droplets. The current approach provides a means to control wettability-driven phenomena.