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This paper reports a miniaturized HPLC (high performance liquid chromatography) column packed with nano-pore beads for flexible medical implants applications. The all-flexible-polymer column capable of integrating with micro/nano-devices on a chip separates biological entities to relax stringent requirements on subsequent detectors and to enable parallel detection in a detector array. The fabricated device has successfully separated a protein mixture using nano-pore beads in a miniaturized column. According to HPLC analysis, the intensity ratio of large to small protein varies significantly, more than a factor of 300, over sample collecting time, ~12mins, suggesting very high separation performance.