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This paper provides a novel micro contact printing system with batch-filling and parallel printing capability for rapid generation of protein arrays. Micro filling chip can simultaneously transfer tens to hundreds of protein solutions into the micro stamp chip in seconds by capillary force without cross-contamination, while maintaining the functionality of proteins before the application. Different proteins can be dispensed into the corresponding channels and driven to the tips of the micro stamps by capillary force passively. The protein-filled micro stamp was then brought into parallel contact print multiple proteins on the substrate to form bio-fluid spot arrays. Teflon patterns laid on the interface of the micro filling chip and the micro stamp chip were employed to prevent cross-contamination during the filling process. Testing results showed that 36 kinds of protein solutions can be parallel printed and the standard deviation of the spot size was under 5%. This system provides a passive, gentle, and high throughput way to simultaneously filling and printing tens to thousands of bio-solution in seconds into a dense array for disease diagnosis or drug screening.