The ultrafast modulation of light in a compact system is an active area of research in many fields, [1][2][3] such as optical communications, inter-electronic chip optical connections, and photonic circuits. The importance of the optical modulation has driven extensive efforts [4][5][6][7][8][9][10][11] in the discovery of new techniques and the optimization of existing techniques of light modulation. We report an all-optical modulation technique based on an opto-mechanical nano-system (OMNS) in which the modulation of the transmitted light is caused by the coherent oscillation of the phonon modes of gold caps on periodic polystyrene (PS) sphere monolayer arrays. The phonon oscillation modes in this two dimensional photonic crystal are generated by excitation with a low repetition rate femtosecond pulsed laser. The coherent phonon oscillation in this system has long decay time allowing for the observation of many modulations. The optical modulation amplitude is two to three orders of magnitude higher than that observed for a thin film or metal nanoparticles. The nanometer thin gold cap is essential in our system because the coherent phonon oscillation modes are generated as a result of its strong and ultrafast photothermal processes taking place following the femtosecond pulsed laser excitation. We demonstrated that the modulation frequency can be tuned by changing the size of the polystyrene spheres. Several techniques have been used to modulate light in optical modulators. One of them uses the quantum-confined stark effect [4,5] which is induced by applying electric fields perpendicular to quantum well layers. The applied electric field separates the electrons and holes within the quantum well layers. The separation of the electrons and holes reduces the excitation energy of electron-hole pairs, thus causing a red shift in the spectrum. By applying periodic electric fields, the light passing through the quantum well layers is modulated accordingly.[5] Experimentally, Lewen et al. [12] have fabricated a device that can modulate light at a frequency higher than 50 GHz. However, the quantum wells with strong quantumconfined stark effect are usually made from III-V semiconductors such as InP, GaAs, and their alloys, which are hard to be integrated with current silicon devices. Recently, a breakthrough is demonstrated in a silicon-based germanium quantum-well structure, which has strong quantum-confined stark effect comparable to the III-V semiconductor structures.