1. A method of processing X-ray image data in an electron probe microanalyzer, said method comprising the steps of: obtaining plural sets of X-ray image data from the same region of a sample at different timings using the electron probe microanalyzer and storing the sets of X-ray image data into memory; simultaneously obtaining sets of electron image data based on detection of secondary electrons or backscattered electrons emanating from said region at said timings and storing the sets of electron image data into memory; comparing the sets of electron image data obtained at the different timings and calculating an amount of positional deviation; and performing an operation for extracting a region common to regions respectively producing the sets of X-ray image data obtained at said different timings on these sets of X-ray image data based on the calculated amount of positional deviation.