The use of focused ion beam (FIB) milling in a cryogenic environment provides an alternative to cryomicrotome for creating submicron sections of frozen hydrated samples. Although FIB milling has been widely implemented to sculpt inorganic sample sections for analysis such as transmission electron microscopy, the application of this technique to frozen biological samples has scarcely begun. The interactions of gallium ions used in FIB with water ice as the target are still not well understood, impeding the development of this technique for routine biological analysis. In this research, amorphous water ice samples are prepared by both vapor deposition and plunge freezing, and the sputtering yield is studied based on a number of process parameters, including ion energy, temperature, and ion current. Results show that sputtering of water ice by gallium ions is a compound process of nuclear sputtering and electronic sputtering. Analytical models, originally limited to astrophysics, are adopted in this study to predict the sputtering yield of water ice by FIB. The parameters for gallium ions at keV range are estimated and validated based on the experimental data. Temperature dependence of sputtering yield is also observed in the range between 83 and 123 K, in which significant increase of sputtering yield occurs when the temperature approaches 123 K. Sputtering yield is not significantly affected by variation of the ion current as shown by the data. Based on these results, the process parameters involved can be characterized, and feasible settings can be developed to facilitate reproducibility and ultimately the widespread implementation of FIB to biological sample preparation. (c) 2008 American Vacuum Society.