In the present study, wettability of focused ion beam (FIB) irradiated hydrophobic FOPA surface was investigated. It was evaluated by contact angle measurement and a chemical composition of surface was analyzed by glow discharged-optical emission spectroscopy. The result shows that the hydrophobicity of the surface decreased after FIB irradiation because fluorine atoms of FOPA were sputtered from the surface. In addition, FIB irradiation was used to fabricate a submicron-scale hydrophilic spots on hydrophobic surface. Condensation behavior was observed by environmental scanning electron microscope and condensed tiny droplets appeared on hydrophilic spots while no droplet are observed on pristine FOPA surface near these spots. Observed result shows that the submicron-scale nucleation behavior can be controlled by surface wettability modification.