Circulating tumor cells (CTCs) refer to cells that detach from a primary tumor, circulate in the blood stream, and may settle down at a secondary site and form metastases. The detection and characterization of CTCs are clinically useful for diagnosis and prognosis purposes. However, there has been very little work on purging CTCs from the blood. In this study, we systematically studied electroporation of tumor and blood cells in the context of selective purging and analysis of CTCs, using M109 and mouse blood cells as models. Electroporation is a simple and effective method for disruption of the cell membrane by applying an external electric field. We applied a microfluidic flow-through electroporation to process cells with various electroporation durations and field intensities. With duration of 100–300 ms, we found that the thresholds for electroporation-induced lysis started at 300–400 V cm−1 for M109, 400–500 V cm−1 for white blood cells and 1100–1200 V cm−1 for red blood cells. Due to the substantial difference, we demonstrated the selective electroporation of tumor cells among blood cells and the scale-up of the flow-through electroporation devices for processing samples of millilitre volumes. Using Coherent Anti-stokes Raman Scattering (CARS) and fluorescence microscopy tools, we observed the dramatic increase in the size of the nucleus of a tumor cell in response to the applied field. We suggest that the nucleus expansion is a newly discovered mechanism responsible for rapid tumor cell death resulted from electroporation.