1. A method for observing defects using a scanning electron microscope, comprising the steps of: setting an imaging region on a specimen where to perform auto focusing a scanning electron microscope on the basis of design information of the specimen; imaging the thus-set imaging region on the specimen plural times at a first magnification while varying the focusing position of the scanning electron microscope in a direction perpendicular to the specimen; 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 at the first magnification while varying the focusing position; imaging the specimen at a second magnification which is lower than the first magnification with the scanning electron microscope using the determined target focusing position information; acquiring position information of a defect detected by an inspection apparatus from an image of the specimen acquired by imaging the specimen at the second magnification; imaging the specimen at a third magnification which is higher than the second 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 third magnification; wherein the step of setting the imaging region is performed to set a plurality of imaging regions where to perform auto focusing for each defect of the defects detected by the inspection apparatus; wherein the step of imaging the thus-set imaging region is performed to image each of the plurality of the imaging regions plural times at the first magnification; and wherein the step of determining target focusing position information is performed to determine by using plural image signals of the plurality of the imaging regions.