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We have investigated fs-laser ablation as well as optoperforation threshold of PDMS (Polydimethylsiloxane) thin lid cover on μ-channel with changing the flow medium from water to hemoglobin. The ablation threshold is found to be independent of both PDMS thin film thickness and flow medium, but the optoperforation threshold is dependent on the films thickness. The observation that the ablation process is well described with simple two-temperature model supposed that the cover lid PDMS of μ-channel be processed with minimized thermal effects by fs-laser with low laser fluence.