Cancer Stem Cells (CSCs) are tumorigenic cells that have characteristics similar to normal stem cells but have ability to generate cells, which are found in the cancer sample. The rare amount of CSC cells in the whole blood makes isolating them from other cells a daunting task. Well defined phenotypes of different CSCs makes immunocapturing technique of CSCs more desirable. A microfluidic device is a proven platform for user constrained microenvironments which can be optimized by small scale volumetric flow experimentation. In this study, we showed a micromixer design (Staggered herringbones) can be optimized to get the maximum chaotic mixing within antibody coated on the microchannels to further capture CSCs. Our device’s design includes the configuration of Staggered Herringbones on top and bottom of the channels (Staggered High Low Herringbones- SHiLoH). It was constructed using polydimethylsiloxane (PDMS) foundation and thinly coated with an alginate hydrogel derivatized with streptavidin. We also compared between the Single walled Staggered Herringbones device and the Staggered High Low Herringbones device with different orientation of the herringbones. The results showed that the micro vortex generated within the micro channels of Staggered High Low design makes the device more efficient than the Single walled staggered Herringbones. Further the non-stickiness of alginate and antigen-specific antibodies can allow better target-specific cell isolation. Our qualitative and quantitative results demonstrate the advancements in cancer stem cell isolation and more comprehensive single-cell and cluster analysis.