Fabrication of a 3D structure and surface texture using excimer laser mask projection ablation processes typically requires the machine operator to develop a specific NC part program for the desired structure geometry, and also incorporate appropriate machine parameters to achieve the desired surface finish. The capability of the laser ablation process could therefore be significantly improved by developing a CAD/CAM system that automatically generates the NC part program using the 3D information of the CAD model of the desired structure. Accordingly, the focus of this research was to develop such a system that is, an effective CAD/CAM system specifically for excimer laser mask projection micromachining tools. To meet these requirements, a unique combination of commercially available systems was used to develop the new CAD/CAM system. The systems used comprised of a computer aided, feature based parametric design system (SolidWorks), together with its extended programming capabilities based on Automated Programming Interface (API) functions for Windows applications, and Visual Basic (VB) 6.0 programming utilities. The system's algorithms use a novel methodology to extract the 3D geometry of a microstructure. Two different techniques have been developed to extract the 3D data. First, where 3D geometry information from a CAD model was defined as a Stereolithography (STL) file, and second, where this information has been contained in a set of bit-map (BMP) files that represent a sliced or layered structure of a CAD model. Based on this, first an algorithm to create NC part programs to support Step-and-repeat micromachining technique was developed and then successfully extended to be applicable for another commonly used micromachining method, Workpiece-Dragging technique. The systems algorithms for both techniques are based on the raster-colour programming technique, resulting in substantially reduced mathematical complexity and computational time. This is the first time this approach has been used to support direct conversion of 3D geometry from a CAD model into an NC part program compatible with the excimer laser CNC controller. 2D mathematical models for controlling edge and stitching errors were also implemented in the system. An additional technique, named as 'Common Nest' has been developed with the aim to enable automatic NC part programming when microstructure design to be completed successfully, requires use of multiple complex mask patterns as a projection tool instead of just a single square aperture. The effectiveness of the system was verified by NC part program generation for several 3D microstructures and subsequent machining trials using polycarbonate (PC) and Polyethylene terephthalate (PET), and optimised processing parameters. Excellent agreement was obtained between the laser machined geometries and the microstructure CAD models. The Laser Scanning Confocal Microscope (LSCM) measured the lateral dimensions tolerance of 2m. The system was also successfully applied for a practical micro-engineering application, for the development of a microfluidics cell transportation device.