1. A method for observing a defect using a scanning electron microscope, comprising the steps of: setting an imaging region on a specimen where to perform auto focusing using a scanning electron microscope on the basis of position information of a defect on the specimen that was detected by a separate inspection apparatus; imaging the thus-set imaging region on the specimen plural times while varying the focusing position of the scanning electron microscope; determining target focusing position information of the scanning electron microscope from plural image signals of the imaging region acquired by imaging the imaging region plural times while varying the focusing position; imaging the specimen at a first magnification with the scanning electron microscope using the determined target focusing position information; acquiring position information of the defect detected by the inspection apparatus from an image of the specimen acquired by imaging the specimen at the first magnification; imaging the specimen at a second magnification which is higher than the first magnification with the scanning electron microscope using the acquired position information of the defect and the determined target focusing position information; and extracting an image of the defect detected by the inspection apparatus from an image of the specimen acquired by imaging the specimen at the second magnification.