We investigated secondary ion mass spectrometry (SIMS) for cellular imaging with high spatial resolution. Cellular level imaging would require nanoscale processing techniques for removal of contamination from cell surfaces and exposing the inner matter of cells. In this study, we applied gas cluster ion beams to the etching of biological samples. Molecular ions were detected with high-intensity from cholesterol samples etched with Ar cluster ions. Additionally, the intensity of secondary molecular ions with gas cluster ion irradiation was compared to that with Au3+ or C60+ beam irradiation and we demonstrated the advantage of using gas cluster ions as etching beams for biological samples with low damage. Finally, we performed etching of animal cells with Ar cluster ions and SIMS analysis of the etched cells. We demonstrated that the cell surfaces were etched with low damage by using gas cluster ion beam.