In the fabrication of micro-electro-mechanical systems (MEMS) devices, manufacturing process variations are usually involved. For these devices sensitive to process variations such as doubly-clamped beams, mismatches between designs and final products will exist. As a result, it underlies yield problems and will be determined by design parameter ranges and distribution functions. Topographical changes constitute process variations, such as inclination, over-etching, and undulating sidewalls in the Bosch process. In this paper, analytical models are first developed for MEMS doubly-clamped beams, concerning the mentioned geometrical variations. Then, finite-element (FE) analysis is performed to provide a guidance for model verifications. It is found that results predicted by the models agree with those of FE analysis. Assigning process variations, predictions for performance as well as yield can be made directly from the analytical models, by means of probabilistic analysis. In this paper, the footing effect is found to have a more profound effect on the resonant frequency of doubly-clamped beams during the Bosch process. As the confining process has a variation of 10.0%, the yield will have a reduction of 77.3% consequently. Under these circumstances, the prediction approaches can be utilized to guide the further MEMS device designs.