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This paper is focused on the design, fabrication and characterization of a continuous flow magnetophoretic microseparator for the separation of selectively tagged cells using para-magnetophoresis. The microseparator was characterized experimentally using head and neck cells lines 212LN and 686LN-M4E as a case study. The microfluidic separation system can separate the selectively tagged cancer cells depending on their membrane protein expression level. Experimental results show that at flow rates of 100 muL/hr and 200 muL/hr, 86.3% and 79.0% of tagged cancer cells were attracted toward center channel respectively, while 95.1% and 87.2% of non-tagged cells remained in the side channels. Additionally, the experimental results of separating tagged cancerous cells from human blood were presented.