A system for analyzing a semiconductor device, including: a first specimen fabricating apparatus including: a vacuum chamber in which a sample substrate is placed, an ion beam irradiating optical system for forming a specimen on the sample substrate, a specimen holder to mount the specimen, and a probe for removing the specimen from the sample substrate; a second specimen fabricating apparatus, and an analyzer to analyze the specimen, wherein said first specimen fabrication apparatus has a function to separate the specimen mounted on the specimen holder and the probe in a vacuum condition.