We developed a processing technique for biological samples, that is, animal cells, for imaging mass spectrometry using gas cluster ion beams. Secondary ion mass spectrometry has been investigated for cellular imaging with high spatial resolution. Nanoscale processing techniques are needed for cellular level imaging, for example, for removing contamination from cell surfaces and exposing the insides of cells. In this study, we compared the mass spectrum of the unetched cell sample to that of the cell irradiated with an Ar cluster ion beam. The contamination was removed from the sample surface and the signals of intracellular components were detected. The results indicate that the cells were etched with low damage using the gas cluster ion beam. Finally, we compared the ion image of an unetched cell to that of an etched cell and demonstrated that the technique of cluster ion irradiation could be applied to the processing of samples for cellular level imaging mass spectrometry.