Shave‐off depth profiling achieves the highly precise depth profiling with nanometre‐scaled depth resolution by using a focused ion beam micro‐machining process to provide depth profile. This method has its own features: absolute depth scale, pinpoint depth profiling and application for rough surface and/or hetero interface. Although this method has significant features, the quantitative evaluation of the fundamental predominance in shave‐off depth profiling is still insufficient because the shave‐off scanning mode has a distinctive position of the primary ion beam against the sample. In this study, the sputtering yield and the mixing effects under the shave‐off scan mode were investigated using molecular dynamics simulation. The obtained sputtering yields under the shave‐off and the raster modes accorded well with experimental results. The results of sputtering yields and root mean square displacement suggested that the shave‐off scan mode has a high sputtering yield and low mixing effects compared with the raster scan mode. In addition, the distribution of the marker atoms clearly showed the process of mixing. Copyright © 2012 John Wiley & Sons, Ltd.