A simple and fast process to fabricate micro-electro-mechanical (MEM) resonators with deep sub-micron transduction gaps in thin SOI is presented. The proposed process is realized on both 350 nm and 1.5 μm thin silicon-on-insulator (SOI) substrates, evaluating the possibilities for MEMS devices on thin SOI for future co-integration with CMOS circuitry on a single chip. Through the combination of conventional UV-lithography and focused ion beam (FIB) milling the process needs only two lithography steps, achieving 100 nm gaps, thus ensuring an effective transduction. Different FIB parameters and etching parameters and their effect on the process are reported.