A microfluidic device (1) comprises a substrate (10) having a flow input channel (30) in fluid connection with a first fluid port (31) and a flow output channel (40) in fluid connection with a third fluid port (41) and cell channels (20) disposed between the flow input channel (30) and the flow output channel (40). The cell channels (20) comprise a respective obstruction (25) designed to prevent the target cells from passing the respective obstruction (25) and into the flow output channel (40). The microfluidic device (1) also comprises a pre-filter (50) with a filter channel (60) in fluid connection with a first filter port (61) and pre-filter channels (70) adapted to accommodate the target cells. A respective first end (72) of the pre-filter channels (70) is in fluid connection with the filter channel (60) and a respective second end (74) of the pre-filter channels (70) is in fluid connection with the flow input channel (30).