A scanning electron microscope comprising: an optical imaging device arranged to optically image a sample; an electron optical system arranged to irradiate the » sample with an electron beam; a first detector for detecting secondary electrons or backscattered electrons emitted in response to the irradiation of the sample with the electron beam; a second detector arranged to detect X-rays or Auger electrons emitted in response to the irradiation of the sample with the electron beam; a scanning electron microscope image generator arranged to generate a scanning electron microscope image, based on an output signal from the first detector; an elemental analyzer arranged to perform elemental analysis based on an output signal from the second detector; a control section arranged to control the electron optical system, the first detector, and the second detector; and an image processor section arranged to cause first markers indicative of imaging positions of the scanning electron microscope image and second markers indicative of analysis positions to be displayed on a display device such that at least one of the first and second markers are placed on a whole image of the sample, wherein said whole image is an image of the sample taken by the optical imaging device; wherein the image processor section is further arranged to operate to alter the magnification of the whole image based on instructions displayed on the display device for altering the magnification of the whole image, characterized in that the image processor section further operates to cause new first markers of the same size and configuration as the first markers placed on the unaltered magnification whole image to be placed on a position corresponding to one of the imaging positions of the scanning electron microscope image on the altered magnification whole image and to cause the scanning electron microscope image in a size according to the altered magnification of the whole image to be placed on a position corresponding to the one of the imaging positions of the scanning electron microscope image on the altered magnification whole image, when the first markers have been placed on the unaltered magnification whole image, and to cause new second markers of the same size and configuration as the second markers placed on the unaltered magnification whole image to be placed on the altered magnification whole image, when the second markers have been placed on the unaltered magnification whole image. an optical imaging device arranged to optically image a sample; an electron optical system arranged to irradiate the » sample with an electron beam; a first detector for detecting secondary electrons or backscattered electrons emitted in response to the irradiation of the sample with the electron beam; a second detector arranged to detect X-rays or Auger electrons emitted in response to the irradiation of the sample with the electron beam; a scanning electron microscope image generator arranged to generate a scanning electron microscope image, based on an output signal from the first detector; an elemental analyzer arranged to perform elemental analysis based on an output signal from the second detector; a control section arranged to control the electron optical system, the first detector, and the second detector; and an image processor section arranged to cause first markers indicative of imaging positions of the scanning electron microscope image and second markers indicative of analysis positions to be displayed on a display device such that at least one of the first and second markers are placed on a whole image of the sample, wherein said whole image is an image of the sample taken by the optical imaging device; wherein the image processor section is further arranged to operate to alter the magnification of the whole image based on instructions displayed on the display device for altering the magnification of the whole image, characterized in that the image processor section further operates to cause new first markers of the same size and configuration as the first markers placed on the unaltered magnification whole image to be placed on a position corresponding to one of the imaging positions of the scanning electron microscope image on the altered magnification whole image and to cause the scanning electron microscope image in a size according to the altered magnification of the whole image to be placed on a position corresponding to the one of the imaging positions of the scanning electron microscope image on the altered magnification whole image, when the first markers have been placed on the unaltered magnification whole image, and to cause new second markers of the same size and configuration as the second markers placed on the unaltered magnification whole image to be placed on the altered magnification whole image, when the second markers have been placed on the unaltered magnification whole image.