The recent attention paid to sample preparation of multilayered structure on glass substrates indicates that cross-sectional transmission electron microscopy (X-TEM) are of considerable interest for their potential effectiveness in thin-film transistor liquid crystal display (TFT-LCD) application. We describe the significant features of our failure analysis problem which involves some difficulties: fragile location, anomalous, and rare defect. An application of focused ion beam (FIB) etching to specimen preparation for X-TEM observation is introduced. We demonstrated that the FIB technique, which allows very localized etching without inducing mechanical stress to thin TEM sample, is very convenient for this delicate location. We also demonstrate that our FIB etching technique is capable of high thinning rates, which allows rapid production of high-quality TEM specimen. Finally, we demonstrate how faulty TFTs including long and fragile protrusions such as whiskers, can be characterized by means of FIB and X-TEM combination.