Single cell detection and analysis offers a new dimension to look for disease related mutations within biological samples. Analyzing samples at the single cell level will give unprecedented information and is necessary for the next frontier in precision, targeted medicine. Current detection mechanisms are often limited by population-averaged studies, potentially missing out on specific disease related mutations critical to understanding or diagnosing the disease properly. Here we present a microfluidic biochip that can isolate single cells efficiently. Our device is effective to minimize cell losses that aids in the sample preparation of rare cell events such as circulating tumor cells (CTCs) in peripheral blood. We had demonstrated that our device was useful to allow sensitive detection of critical mutations linked to drug response, which would otherwise be missed out in bulk analysis. In our preliminary clinical study, we revealed that CTC counts within lung cancer patients were limiting and the dominant EGFR mutations such as L858R and T790M were present within these CTCs. It also highlighted the heterogeneous nature of the disease as not all cells carry these mutations. We envision the biochip will enable efficient isolation of rare single cell samples and coupled with downstream molecular characterization of CTCs will aid in realizing the personalized medicine for cancer patients.