Microfuel cells are a possible replacement for batteries as energy sources in portable devices. At PSI a micropolymer electrolyte fuel cell was developed, whose flow fields consist of micro-structured glassy carbon plates. Micro-structuring of glassy carbon is carried out in a multi-step process. A sputtered aluminum mask is selectively removed by single pulse laser ablation from glassy carbon thereby defining micro-channels subsequently etched by reactive ion etching. A pulsed XeCl excimer laser (308 nm) is used for the single pulse patterning of a metal mask on the glassy carbon. The influence of the excimer laser typical pulse to pulse energy fluctuations on the micro-structuring process must be known to minimize defects during RIE etching of the micro-channels. To obtain a better understanding of the processes occurring during ablation, ns-shadowgraphy was performed. The formation of a shockwave was observed, followed by a similar but much slower perturbation, and the subsequent release of fragments. The calculated velocities can be correlated with the energy release during ablation. The post-ablation examination of the samples by profilometry, optical microscopy, SEM and EDX is used to measure the amount of removed material, the quality of the aluminum mask edges and aluminum residues on the glassy carbon surface. Such criteria allow us to classify the laser irradiation as a function of laser fluence: no ablation, partial ablation, complete ablation, and over-ablation. (C) 2008 Elsevier B. V. All rights reserved.