In this work the results obtained in experimental studies of conditions of the nanoscale profiling of a silicon substrate surface under the ion stimulation of W and Pt deposition by a Ga+ ion beam are represented. It is shown that, according to combinations of process conditions, deposition, or etching processes, conditions of the formation of transition structures can also be implemented. It is found that the rate of ionstimulated deposition of W and Pt averages 8 nm/min and 50 nm/min for ion-beam currents of 2.3 pA and 7.9 pA, respectively, and the rate of ion-beam etching of a silicon substrate is 6 nm/min and 55 nm/min for ion-beam currents of 2.3 pA and 111.4 pA respectively. With the use of these results, the modes are determined and a prototype of sensing element of tunnel accelerometer is formed using focused ion beams (FIBs). The results can be used to develop manufacturing methods of generating patterns of nano- and microelectronics and nano- and microsystem engineering on the basis of FIBs.