This paper describes computer-aided design tools for micro-mechanisms that help designers validate correct function, detect design flaws, and assess the effects of part clearances. The domain characteristics of curved geometry, joint play, and higher pairs render traditional software inappropriate. Our software uses configuration spaces to model the kinematic function of micro-mechanisms. It uses the configuration spaces to perform real-time simulation, to compute functional kinematic tolerances, and to support parametric design. Designers can visualize system function under a range of operating conditions, can find and correct design flaws, and can optimize dynamical function. The software is demonstrated on a surface micromachined counter meshing gear discrimination device developed at Sandia National Laboratory.