To provide an electron beam system capable of performing three-dimensional measurement of a sample with high precision irrespective of the tilt angle and height of the sample. The electron beam system has a correction factor storing section 32 for storing a correction factor at a reference tilt angle with respect to a plane which is used to tilt a sample by a sample tilting section 5, an approximate coordinate measuring section 28 for obtaining an approximate shape or approximate coordinate values of the sample based on an output corresponding to a stereo image from an electron beam detecting section 4, an image correcting section 30 for correcting the stereo image according to the tilt angle created by the sample tilting section 5 based on the shape or coordinate values of the sample obtained in the approximate coordinate measuring section 28 using a correction factor stored in the correction factor storing section 32, and a precise coordinate measuring section 34 for obtaining a shape or coordinate values of the sample which are more precise than those obtained in the approximate coordinate measuring section 28 based on a corrected stereo image obtained in the image correcting section 30.