A 3D CAM tool for rapid prototyping and small-scale production of MEMS devices based on excimer laser ablation process has been developed. The system’s algorithms use the 3D geometry of a microstructure, defined in a CAD model, and parameters that influence the process (etch rate, wall angle, stitching errors, etc.) to automatically generate a precise NC part program for the excimer laser machine. The performance of the system has been verified by NC part program generation for several 3D microstructures and subsequent machining trials. Stitching errors of 23.4±2.2 μm wide and 3.4±1.5 μm height were observed when overlap size between adjacent volumes were zero, when ablating 100×100 μm features in PC at fluence of 0.9 J/cm2 using a workpiece dragging technique. When the size of the overlap was optimised by software based on optimal process parameters determined by Taguchi design of experiment method (DOE) and incorporated in the mask design the maximum stitching errors are reduced to 13.4±2.2 μm wide and 1.4±0.9 μm in height under the same conditions. Employing the hexagonal shaped mask with incorporated size of the image overlap, horizontal-stitching errors with width of 2.4±0.2 μm wide and 1.4±0.2 μm high were observed. The software simplifies part program creation and is useful for excimer laser operators who currently use a tedious trial and error process to generate microstructure parts.