In characterization or failure analysis of new materials and semiconductor devices, the requirements for three dimensional observation and analysis are rapidly increasing. We discuss techniques for specimen preparation, three-dimensional observation, and elemental analysis of semiconductor devices that we developed using a system consisting of a dedicated focused ion beam (FIB) instrument and a scanning transmission electron microscope (STEM). The system utilizes a FIB-STEM compatible specimen holder with a specially designed rotation mechanism, which allows 360° rotation of a specimen on a conical stage (needle stub) around the ion beam axis of the FIB system and 360° rotation perpendicular to the electron beam in the STEM. A piece of sample (micro sample) is extracted from a specific-site by the micro-sampling technique and mounted on the needle stub. Instruments used in the study are the Hitachi FB-2100 FIB system with a micro-sampling attachment and the HD-2300 field emission 200kV STEM.