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In this paper, we report a silicon/glass based micro fuel cell system fabricated by the micromachining technique. The anode and cathode catalyst layers are formed by directly sputtering platinum on the ICP-etched (Inductively Coupled Plasma) high-aspect-ratio columns on silicon substrate. Integrated gold-based micro current collectors are patterned on the silicon and glass surfaces. This prototypical micro fuel cell fed by H2/O2 demonstrates an output power of 7.10 mw/cm2. An improved power of 12.3 mW/cm2 is achieved by a novel etching process. Both prototypes are also tested with methanol/O2, and the maximum output power is 0.10 mW/cm2 and 0.15 mW/cm2, respectively. Low internal resistance (around 0.7Ω·cm2) is achieved when using thin gold film (200 nm) as current collectors and the catalyst surface roughness does not affect the internal resistance.