A new direct laser patterning system for improving the quality of the pattern on the glass substrate of large Flat Panel Displays (FPD) was developed, which consists of the laser machining center, the laser measurement system, and the adaptive rotational mirror system. The new system is distinguished from the existing system by its control mechanism which compensates for the laser beam error caused by the volumetric error of the multi-axis machine. The new system, in comparison with existing systems which control each stage of multi-axis, uses a fast steering mirror (FSM) and adaptive laser optics to compensate for the error of the laser beam on the substrate. Through this study, a mathematical model of the volumetric error of the multi-axis laser machining center was developed to quantify the geometric and the kinematic errors of each machine axis and their contributing effect on the substrate. The information contained in the mathematical model was expressed in a volumetric error matrix. Further, a mathematical model of the beam delivery was developed to measure the beam delivery on the substrate and its effect on the quality of the patterning. The patterning errors were corrected by using an FSM, which has two rotational angles. The viability of the proposed scheme was demonstrated through simulations and experiments.