The present invention relates to an automatic sequence for repeatedly performing SEM observation and FIB processing by using a low acceleration voltage for a long time. In order to realize very accurate three-dimensional structure/composition analysis, in the automatic sequence for repeatedly performing sample observation using a scanning electron microscope using a CFE electron source and sample processing using a FIB device, low temperature flushing using the CFE electron source is performed at predetermined timing except for a SEM observation time. According to the present invention, the automatic sequence for repeatedly performing the sample observation using the scanning electron microscope using the CFE electron source and the sample processing using the FIB device can be performed for a long time. Therefore, it is possible to acquire a SEM image which achieves high resolution and improved current stability while the low acceleration voltage is used.