Maskless etching approaches such as microdischarges and atmospheric pressure plasma jets (APPJs) have been studied recently. Nonetheless, a simple, long lifetime, and efficient maskless etching method is still a challenge. In this work, a separated type maskless etching system based on atmospheric pressure He/O2 plasma jet and microfabricated Micro Electro Mechanical Systems (MEMS) nozzle have been developed with advantages of simple-structure, flexibility, and parallel processing capacity. The plasma was generated in the glass tube, forming the micron level plasma jet between the nozzle and the surface of polymer. The plasma microjet was capable of removing photoresist without masks since it contains oxygen reactive species verified by spectra measurement. The experimental results illustrated that different features of microholes etched by plasma microjet could be achieved by controlling the distance between the nozzle and the substrate, additive oxygen ratio, and etch time, the result of which is consistent with the analysis result of plasma spectra. In addition, a parallel etching process was also realized by plasma microjets array.