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Micro-opto-electromechanical systems (MOEMSs) are a new class of integrated and miniaturized optical systems that have significant applications in modern optics. However, the integration of micro-optical elements with complex morphologies on existing micro-electromechanical systems is difficult. Herein, we propose a femtosecond-laser-assisted dry etching technology to realize the fabrication of silicon microlenses. The size of the microlens can be controlled by the femtosecond laser pulse energy and the number of pulses. To verify the applicability of this method, multifocal microlens arrays (focal lengths of 7–9 μm) were integrated into a silicon microcantilever using this method. The proposed technology would broaden the application scope of MOEMSs in three-dimensional imaging systems.