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The functioning of many micro-electromechanical devices with parts oscillating at high frequencies require isolation from external vibration. Phononic crystals, presenting band-gaps in the dispersion spectrum, i.e., interval of frequency in which propagating waves are attenuated, can provide an effective solution for vibration shielding at the microscale. In the present work, we design—through numerical simulations—a 3D phononic crystal with a micrometric unit cell able to work as vibration isolator for a micro system. We exploit the direct writing technique based on two-photon polymerization to realize three prototypes of different dimensions. Experimental measurements performed with a Michelson interferometer demonstrate the effectiveness of the proposal.