Fabrication imperfections strongly influence the functioning of Micro-Electro-Mechanical Systems (MEMS) if not taken into account during the design process. They must be indeed identified or precisely predicted to guarantee a proper compensation during the calibration phase or directly in operation. In this work, we propose an efficient approach for the identification of geometric uncertainties of MEMS, exploiting the asymptotic homogenization technique. In particular, the proposed strategy is experimentally validated on a MEMS filter, a device constituted by a complex periodic geometry, which would require high computational costs if simulated through full-order models. The complex periodic structure is replaced by an equivalent homogeneous medium, allowing a fast optimization procedure to identify imperfections by comparing a simplified analytical model with the experimental data available for the MEMS filter. The actual over-etch, obtained after the release phase, and the electrode offset of a fabricated MEMS filter are effectively identified through the proposed strategy.