A method and apparatus are disclosed here for rare target cell enrichment and isolation, where the captured target cells can be individually picked up and used for downstream analysis. This method and apparatus utilize antibodies conjugated microbeads to isolate target cells, use ON/OFF controls for the target cell capturing magnet and the release magnet, such that there is no need to change the cap of the capturing magnet and thus enabling automatic multiple rounds of capturing, washing and releasing cycles to increase the target cell detection sensitivity and reproducibility. A special filter is utilized to effectively remove more than 95% of free unbound microbeads, thus significantly improving the purity of the collected target cells and increasing the data quality of downstream analysis of the single target cells. Lastly, RNA expression patterns are proposed for identifying of certain target cells (e.g. circulating tumor cells and white blood cells).