Present paper uses Direct Simulation Monte Carlo method to perform a numerical study of a new MEMS-based gas separation device prototype. The core part of the device is represented by a microchannel with a row of elements-barriers oscillating with high frequency perpendicular to channel axis and periodically blocking the flow. The influence of practical aspects (device geometry, arrangement of phases of barriers oscillation, gas leakage and etc.) on separation performance was investigated. It is demonstrated that separation factor of the device can approach values of free-molecular (Knudsen) diffusion at any rate of gas rarefaction (defined by Knudsen number) and feasible barriers oscillation frequency (below 10 kHz) given that the necessary number of barriers is used in the device. Moreover, it was shown that in case of partial sampling of gas at the outlet, separation factor of the device can increase significantly beyond the Knudsen diffusion limit.