With the increase of thrust-weight ratio of aero-engine, the working temperature of core parts is becoming higher and higher. In order to improve the service life of core parts, many high-precision micro holes are machined on those core parts. To realize the fabrication of micro hole with less burrs on super alloy substrates, a novel water jet guided laser processing method is proposed in this paper. A material removal principle based on plasma detonation assistant machining is proposed and proved to be valid through experiments. Then a laser-induced plasma assisted ablation method using sacrificial layer in the machining of through holes and grooves on super alloy is approved. This method can get higher machining efficiency and avoid longtime trimming in subsequent experiments. The size of burrs in through hole decreases 57.89%, while the area of burrs decreases 42.32% after using 304 stainless steel as sacrificial layer in the machining of through hole. Grooves with fewer burrs are also achieved on super alloy with this method. That method can also be used to fabricate a variety of functional structures.