A plasma cleaner is usually used for removing carbonaceous debris from a specimen and preventing contamination during transmission electron microscopy (TEM) imaging and analysis. However, the plasma cleaner can be effectively used for thinning down damage layers on TEM specimens prepared by focused ion-beam (FIB) milling. By optimizing plasma treatment conditions, the quality of high-resolution images and diffraction patterns of the FIB-milled specimens has been remarkably improved using the plasma cleaner.