A method of quite efficiently analyzing contaminants such as dust on a semiconductor material with a scanning electron microscope. The instrument holds a list of data about contaminants. The operator selects desired items from the list and marks them to register them in a registered contaminant data table. Then, he establishes illumination conditions used for analysis and starts x-ray analysis. A secondary electron image of any contaminant of interest is displayed on a CRT at a magnification corresponding to the dimensions of the contaminant. The dimensions are retrieved from the data table. All addresses of a frame memory are searched. According to the results, the coordinates of the position of the contaminant are measured. The difference between the central position of the viewing screen of the CRT and the coordinate of the contaminant is calculated for each direction. The calculated differences are sent either to a specimen stage-driving mechanism or to an image shift power supply. In this way, the contaminant is automatically centered. The focused electron beam is directed at the center of this contaminant to produce x-rays. If the analysis of this wafer is not yet complete, data about the next contaminant item is retrieved from the registered contaminant data table.