Laser micromachining has great potential as a MEMS (micro-electro-mechanical systems) fabrication technique because of its materials flexibility and 3D capabilities. The machining of deep polymer structures with complex, well-defined surface profiles is particularly relevant to microfluidics and micro-optics, and in this paper we review recent work on the use of projection ablation methods to fabricate structures and devices aimed at these application areas. In particular we focus on two excimer laser micromachining techniques that are capable of both 3D structuring and large-area machining: synchronous image scanning (SIS) and workpiece dragging with half-tone masks. The methods used in mask design are reviewed, and experimental results are presented for test structures fabricated in polycarbonate. Both techniques are shown to be capable of producing accurately dimensioned structures that are significantly deeper than the focal depth of the projection optics and virtually free from fabrication artifacts such as the steps normally associated with multiple-mask processes.