Scanning capacitance microscopy (SCM) has become a valuable tool for failure analysis in integrated circuit manufacture. The ability to perform two-dimensional dopant distribution analysis on small, specific structures has been hampered, however, by the imprecision of current polishing techniques. Utilization of focused ion beam (FIB) milling instrumentation to perform precise cross sectioning of specific structures is preferable to manual polishing, although SCM data has not been forthcoming, due in part at least to the thicker amorphous silicon layer. This work examines the thickness of the amorphous silicon layers generated by various sample preparation methods, including conventional polishing, FIB milling, and low-energy FIB milling. In addition, this work provides SCM comparisons of the low energy FIB milling preparation procedure and conventional polishing.