Method and system for preparing samples for use in electron microscopy. The method and system use a focused ion beam (FIB) instrument and a scanning electron microscope to improve the time efficiency of the FIB instrument. The FIB instrument incorporates machining means for preparing thin-film samples by ion beam irradiation. The scanning electron microscope incorporates a gas supply means and a manipulator equipped with a probe. The gas supply means ejects gas at the sample after it has been shifted from the FIB instrument together with a sample holder. The sample is irradiated with an electron beam while the gas is injected at the sample from the gas supply means under the condition where the probe is contacted with the sample. Thus, the sample is bonded to the probe.