Laser micro-machining is a promising manufacturing solution for fabricating complex micro-engineering products in wide range of materials that incorporate different multi-scale functional features. Optical beam deflector systems are key components in laser micro-machining systems, and they are one of the main factors determining the processing speed and hence machining throughput. However, their performance is speed dependent and the negative dynamics effects have a direct impact on the laser micro-machining accuracy, repeatability and reproducibility. This article presents a generic software solution for minimising these negative dynamics effects, thus improving significantly the laser machining performance across the full range of available processing speeds. In particular, these improvements are achieved by introducing machine-specific compensations in machining vectors to counteract beam deflectors’ inertia regardless of their directions, length and set process speed. An empirical model was developed to obtain data about the actual dynamic response of the beam deflection system across the full range of available processing speeds, and then based on these data, the proposed generic software was implemented into a stand-alone ‘adaptive’ postprocessor. The generation of machine executable part programs is automated, and it is only necessary for the user to enter the selected scanning speeds and beam diameters. Experimental validation was conducted to demonstrate the capability of the proposed software tool. The results demonstrate that substantial improvements can be obtained in machining quality by maintaining a constant pulse distance throughout the machining operations, while the dimensional accuracy is maintained across the available processing speeds without sacrificing the machining efficiency.