The development of new processes for the micro-treatment of material is the basis for increasing integration and miniaturization of mechanical, optical and electronic components. Pulsed high power excimer lasers offer in combination with a micro-machining system, the possibility of manufacturing highly complex components in different materials like ceramics, glass or metals, Because of the increasing number of technical applications, the need for automatic processing has grown in the last few years. While complete working stations are available for Nd:YAG and CO2 lasers, there is a lack for automatic micro-removal with excimer lasers. For complex microstructures like micro- optics, manual programming of the workpiece handling system becomes uneconomic because of the very high number of laser pulses required. Especially for prototypes and small batches where the workpiece geometries change quickly, the development of a universal and automatic machining concept plays a key role for this technology. For this reason, a general machining concept based on excimer laser removal has been realized beginning with the possibility to construct the workpiece geometry by CAD-design tools. A preprocessor allows to calculate the removal volume based on laser specific ablation volumes. The superposition of each laser pulse removal leads to complex 3D surface structures. Moreover, a general movement strategy optimizes the processing speed. For closing the process chain the realized preprocessor automatically generates the necessary NC-data for the implemented CNC-control system. Functionality of this concept has been proven by manufacturing different two and three dimensional micro-structures like micro-optical components.