This paper presents a bio-mimetic microfluidic device that mimics the high compliance and the beating frequency of biological cilia in order to achieve bio-compatible manipulation of microfluidics. Because the highly compliant cilia can easily collapse due to interaction energy and surface tension, the major challenge in developing a bio-mimetic device is the manufacturing of highly compliant cilia. An underwater fabrication method is developed to avoid the cilia collapse by lowering the surface energy of the cilia. Another challenge is to mimic the low beating frequency (10–100 Hz) of biological cilia. The proposed microfluidic device is excited by a piezo actuator to resonate the cilia in water. Due to the highly compliant nature of the silicone cilia, the resulting actuation frequency is in the beating frequency range of biological cilia. Simulations and experiments are presented to demonstrate microfluidic manipulation by resonance of the assembled cilia array.