Focused ion beam (FIB) milling has been widely used for the preparation of cross-sectional transmission electron microscopy (X-TEM) specimens. In FIB fabrication, a protective layer is normally formed on the specimen surface by ion-beam-assisted metal deposition to avoid the damage caused by highly accelerated ion beams. However, the metal deposition itself induces damage in the specimen. This problem is especially serious when the region near the surface of a specimen is of interest. Investigation of : subsurface damage through X-TEM observations showed that, for 30 keV FIB, the defects induced by ion-beam-assisted deposition extend about 400 Angstrom from the surface. In the case of single-crystalline silicon, a several-hundred-angstrom layer just below the surface is converted into an amorphous layer. We propose the use of a plasma-polymerized organic film which is formed by plasma polymerizing of methane and ethylene, instead of the metal deposit. We used the film as a protective layer and fabricated TEM specimens without damaging the fine subsurface structures. In the case of Single-crystalline silicon, no amorphous layer was observed. In addition, a subsurface structure in an aluminum sample prepared by the FIB method was successfully observed by TEM.