Presented is a novel flow manipulation and particle detection method for the microfabricated fluorescence-activated cell sorter (μFACS). With hydrodynamic flow manipulation which includes passive flow channeling and hydrodynamic actuation with nozzle flow, we have developed a fast and robust method for utilizing the sorting function. These techniques are directly related to enabling the high throughput screening of the FACS machine. Moreover by detecting with synchronized imaging, we have also developed an on-line calibration technique for the accurate timing between detection and actuation. And this means that our system is very flexible that it can be tuned to any assay conditions with various flow speeds, particle densities and buffer or sample viscosities by real time calibration.