An excimer laser incorporating a reconfigurable intelligent pinhole mask (IPM) is demonstrated for the fabrication of microfluidic geometries on a poly(methyl methacrylate) substrate. Beam reconfiguration techniques are used to overcome some of the drawbacks associated with traditional scanning laser ablation through a static mask. The production of zero lead-in (ZLI) features are described, where the ramp lead-in angle-inherent to scanning laser ablation-is reduced to be in line with the cross-sectional side-wall angle of the microchannel itself. The technique is applied to eliminate under-cutting and ramping at channel junctions-features resulting from scanning ablation through a fixed mask-and produce flat crossing sections, junctions and inlets. The development of a prediction model for microchannel visualisation and refinement prior to the fabrication step is also described. The model includes variables from the IPM, laser, scanning stage and material etch rate allowing quantitative measurement of generated microchannel geometry. One application of the model is the development of microchannel mixing geometry which is analysed using computational fluid dynamic (CFD) techniques. For this purpose, the effect of varying the overall channel geometry on mixing within a microchannel was investigated for flows with low Reynolds numbers. The resulting geometry is found to reduce the distance required for mixing by 50% in comparison to a straight planar channel, thereby enabling smaller device geometries.