1. A method for extracting three-dimensional data of an object using an electron microscope, the method comprising: obtaining two-dimensional coordinates by respectively projecting the object on a plane perpendicular to an X-axis, on a plane perpendicular to a Y-axis, and on a plane making an angle of 45 degrees from a Z-axis with a Y-Z plane, in an XYZ coordinate system; in portions where three images including the two-dimensional coordinates overlapped, obtaining data of a pixel on a base images among the three images, obtaining data of corresponding pixels of the pixel on the base image to left and right images of the base image, and calculating a disparity on the basis of the data; and extracting three-dimensional depth information of the object using the obtained disparity, the three-dimensional depth information representing a relative distance of the object, and extracting a three-dimensional coordinate on each pixel to determine a three-dimensional location of the object.