We present the development of CMOS compatible focused ion beam (FIB)-based method for the fabrication of nanomechanical devices. With only two step process, (i) patterning by direct exposure of silicon by the gallium beam and (ii) transfer of features to the structural layer by standard microfabrication silicon etching processes, operational devices are obtained. The ion beam modified silicon, acting as the etching mask, presents an outstanding robustness for both chemical and reactive ion etching process, enabling a simplified fabrication of nanomechanical devices with sub-micron resolution. As an example, single and double clamped silicon beams have been successfully produced. The compatibility check to guarantee the integrity of the electronic performance of CMOS circuits after the energetic beam irradiation is also investigated. Patterning based on direct ion beam exposure of silicon and etching presents advantages in comparison with more conventional lithography methods, such as electron beam lithography, since it is realized without the use of any resist media, which is especially challenging for the non-flat CMOS pre-fabricated substrates.