Depth profiling of sucrose thin films was investigated with time-of-flight secondary ion mass spectrometry (TOF-SIMS) using 10 keV C(60)(+), 20 keV C(60)(2+), and 30 keV C(60)(3+), and 250, 500, and 1000 eV Cs(+) and O(2)(+) as sputtering ions. With C(60)(n+) ions, the molecular ion signal initially decreases and reaches a steady state that is about 38-51% of its original intensity, depending on the energy of the C(60)(n+) ions. In contrast, with Cs(+) and O(2)(+) sputtering, molecular ion signals decrease quickly to the noise level, even using very low-energy (250 eV) ions. In addition, the measured width of the sucrose/Si interface is much narrower using C(60)(+) ions than that using Cs(+) or O(2)(+) ions. To understand the mechanisms of sputtering-induced damage by these ions, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) were used to characterize the bottoms of these sputter craters. XPS data show very little chemical change in the C(60)(+) sputter crater, while considerable amorphous carbon was found in the O(2)(+) and Cs(+) sputter craters, indicating extensive decomposition of the sucrose molecules. AFM images show a very flat bottom in the C(60)(+) sputter crater, while the bottoms of the Cs(+) and O(2)(+) sputter craters are significantly rougher. We used the sputtering model developed by Wucher and co-workers to quantitatively analyze our C(60)(1-3+) data. The results show that low energy C(60)(+) ions generate a relatively thin damage layer with a high molecular ion signal, suggesting that low energy C(60)(+) may be the optimal choice for molecular depth profiling of sucrose films.