Semiconductor devices with complicated structures have been developed, and it is becoming increasingly important to understand three-dimensional (3D) structures of devices with nanometer resolution. The key to successful nanometer-scale 3D analysis is sample preparation technology and it has been highly developed. By combining or correlating multiple physical analyses, limitations of single analysis method are well covered and new information of 3D devices is obtained. Simultaneously acquired multi-signal STEM images are effective for internal structure analysis of 3D devices.