We developed a method for patterning organic light emitting molecules with polyaniline(PANI) microstructure as a template.Its microstructure was characterized with atomic force microscopy(AFM).PANI microstructure was treated with O2 plasma at low power and short time to get the hydroxyl groups on the silicon substrate,meanwhile,which can minimize the impact on PANI structure.We modified the structure with fluoro-silane reagent through self-assembly to make substrate bearing different surface energies on different areas.Finally,we deposited dyes on substrate by evaporation.The results show that the dyes on the fluoro-silane monolayer can move toward the PANI structure during storage duration and form the structure of organic light emitting molecules.