A simple and fast process for micro-electromechanical (MEM) resonators with deep sub-micron transduction gaps in thin SOI is presented in this paper. Thin SOI wafers are important for advanced CMOS technology and thus are evaluated as resonator substrates for future cointegration with CMOS circuitry on a single chip. As the transduction capacitance scales with the resonator thickness, it is important to fabricate deep sub-micron trenches in order to achieve a good capacitive coupling. Through the combination of conventional UVlithography and focused ion beam (FIB) milling the process needs only two lithography steps, enabling therefore a way for fast prototyping of MEM-resonators. Different FIB parameters and etching parameters are compared in this paper and their effect on the process are reported.