A technique to characterize specific site of materials using a combination of a dedicated focused ion beam system(FIB), and Intermediate-voltage scanning transmission electron microscope(STEM) or transmission electron microscope(TEM) equipped with a scanning electron microscope(SEM) unit has been developed. The FIB system is used for preparation of electron transparent thin samples, while STEM or TEM is used for localization of a specific site to be milled in the FIB system. An FIB-STEM(TEM) compatible sample holder has been developed to facilitate thin sample preparation with high positional accuracy Positional accuracy of $0.1{\mu}m$ or better can be achieved by the technique. In addition, an FIB micro-sampling technique has been developed to extract a small sample directly from a bulk sample in a FIB system These newly developed techniques were applied for the analysis of specific failure in Si devices and also for characterization of a specific precipitate In a metal sample.