Efficient isolation strategies not based on epithelial biomarker expression are required to enable non-biased enrichment of circulating tumor cells (CTCs). CTCs undergoing epithelial-mesenchymal transition (EMT) may be prognostically relevant, and importantly are not detected with conventional epithelial based approaches such as CellSearch®. A method for the non-biased isolation of cancer cells within a peripheral blood sample utilizing microfluidic mixing PDMS devices functionalized with anti-CD45 is reported. The introduction of micro and nanoscale roughness using a single step treatment with sulfuric acid significantly increases the binding yield of white blood cells (WBCs) to the anti-CD45 conjugated surfaces. Up to 99.99% WBC depletion is achieved with a tumor cell recovery yield of 50%. This high level of CTC enrichment is expected to facilitate the detailed characterization of CTCs using for instance, imaging flow cytometry as demonstrated here.