We demonstrated direct fabrication of a diffraction grating onto organic oligomer crystals by focused ion beam (FIB) lithography followed by argon/oxygen plasma etching. Surface analysis suggested that FIB irradiation broke the oligomer molecules near the crystal surface to form a carbonized layer resulting in emission quenching. The plasma etching removed the damaged layer near the crystal surface and successfully recovered the emission. This technique was applied to fabricate the diffraction grating onto organic oligomer crystals and provided diffracted peaks in their fluorescence spectra without significant emission quenching.