The shearing process for the sheet metal is normally used in the precision elements such as semi-conductor components. In these precision elements, the burr formation brings a bad effect on the system assembly and demands the additional de-burring process, so this imposes high cost on manufacturing. In this paper, we have developed the in-situ auto-aligning precision meso-punching system to investigate the burr formation mechanism and ultimately minimize burr. Firstly, we introduced the punch-die contact sensing method to align the punch and the die at initial state prior to the punching process. Secondly, by using the low-price semi-conductor laser, burr formed on the edges is measured intermittently during the punching process. We could, finally, make burr on the sheet metal uniformized and minimized by controlling of the precision X - Y table, $1\;{\mu}m$ resolution, and measuring burr height by semiconductor laser. Experimental results show the validity of our system for pursuing the burr-free punched elements.