A system for analyzing a semiconductor device, including: a first ion beam apparatus including: a sample stage to mount a sample substrate; a vacuum chamber in which the sample stage is placed; an ion beam irradiating optical system to irradiate the sample substrate; a specimen holder that accommodates a plurality of specimens separated from the sample substrate by the irradiation of the ion beam; and a probe to extract the separated specimen from the sample substrate, and to transfer the separated specimen to the specimen holder; a second ion beam apparatus that carries out a finishing process to the specimen; and an analyzer to analyze the finished specimen, wherein the first ion beam apparatus separates the specimen and the probe in a vacuum condition.