The ultimate goal of the failure analysis process is to find physical evidence that can identify the root cause of the failure. Transmission electron microscopy (TEM) has emerged as a powerful tool to characterize subtle defects. This article discusses the sample preparation procedures based on focused ion beam milling used for TEM sample preparation. It describes the principles behind commonly used imaging modes in semiconductor failure analysis and how these operation modes can be utilized to selectively maximize signal from specific beam-specimen interactions to generate useful information about the defect. Various elemental analysis techniques, namely energy dispersive spectroscopy, electron energy loss spectroscopy, and energy-filtered TEM, are described using examples encountered in failure analysis. The origin of different image contrast mechanisms, their interpretation, and analytical techniques for composition analysis are discussed. The article also provides information on the use of off-axis electron holography technique in failure analysis.