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 co-integration 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 UV-lithography 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.