As industry of PCB (Printed Circuit Board) and display growing, this industry requires an increasingly high-precision quality so current cutting process in industry is preferred laser machining than mechanical machining. Now, laser machining is used almost “step and repeat” method in large area, but this method has a problem such as cutting quality in the continuity of edge parts, cutting speed and low productivity. To solve these problems in large area, on-the-fly (stagescanner synchronized system) is gradually increasing. On-the-fly technology is able to process large area with high speed because of stage-scanner synchronized moving. We designed laser-based high precision system with on-the-fly. In this system, we used UV nano-second pulse laser, power controller and scanner with telecentric f-theta lens. The power controller is consisted of HWP(Half Wave Plate), thin film plate polarizer, photo diode, micro step motor and control board. Laser power is possible to monitor real-time and adjust precision power by using power controller. Using this machine, we tested cutting of large area coverlay and sheet type large area PCB by applying on-the-fly. As a result, our developed machine is possible to process large area without the problem of the continuity of edge parts and by high cutting speed than competitor about coverlay.