Excimer Laser Ablation is a micro-machining method which has undergone an important breakthrough in the last twenty years. In contrast with most literature studies, dealing with Static Ablation, this PhD work focuses on the study of Scanning Ablation of poly(ethylene terephthalate) (PET) at 193 nm, using relatively high fluences of about 1 J/cm2. Here, Static Ablation means that the substrate is fixed with respect to the laser beam. In this way, the size of the machined area per set of pulses does not exceed a few mm2. Moving the substrate under the laser beam during the irradiation, i.e. using Scanning Ablation, enables to machine more easily and with a better quality bigger surfaces. This is particularly interesting for micro-channel prototyping in PET (typical cross-section of the channels: 40×40 µm2, length: >1.5 cm), which was the aimed application of this work. The surface properties of the ablated micro fluidic channels were studied, comparing Static Ablation to Scanning Ablation with different parameters. For this purpose SEM, TEM, XPS, water condensation experiments and electroosmotic flow measurements in laminated micro-channels were carried out. The properties of the ablated surfaces were shown to be modified, in terms of chemical properties and in terms of morphology. In order to explain the modified surface properties after Scanning Ablation, the angle between the irradiated ramp, forming under the beam, and the non irradiated surface was shown to be one key-parameter, the shape of the laser spot on the substrate being the other one. The chemical composition of the ablated surfaces depends on the nature and amount of redeposited debris. There are two types of debris: Indirect debris, which is produced by collision of the ejected material with the ambient atmosphere. After ablation in air, this debris is hydrophilic due to the oxygen and nitrogen content. The geometry of the debris covered area, and thus the amount of indirect debris in the micro channels, depends on the geometry of the irradiated area. Direct debris, which is produced by a mechanism very similar to Pulsed Laser Deposition, is only possible in Scanning Ablation. It is directly ejected in the direction of the channel surface and it is less influenced by the surrounding atmosphere. Condensation experiments proved it to be more hydrophobic than indirect debris. In Static Ablation, only indirect debris is present, and the debris affected surfaces are therefore hydrophilic. In Scanning Ablation, the amount of direct and indirect debris vary differently with the ramp angle and the shape of the irradiated spot. When increasing the ramp angle from 0° to 45°, a maximum electroosmotic flow velocity is measured around 4.3°, which is explained by a maximum of the ratio indirect / direct debris for this angle. Electroosmotic flow velocity measurements in channels of the same width but with different depths (polyethylene laminated), combined with a numerical implementation of an analytical formula for the flow velocity profile, enabled to calculate the ζ-potentials of the ablated the surfaces for different ramp angles and the ζ-potential of the lamination. Besides the chemical composition, Scanning Ablation also changes the morphology of the ablated surfaces. At high ramp angles, the surface structure of the channel floor is determined by the direct debris redeposition leading to a nanometric roughness. The micrometric roughness, which is known to develop in stretched polymer substrates upon Laser Ablation, depends on the ramp angle θ during channel fabrication. As the ramp is the only irradiated surface in scanning ablation, it was studied in detail. Three different structures were observed on ramps in stretched polymer substrates, each in one of three distinct ranges of ramp angles. On the basis of a vector decomposition of the fabrication induced stresses in the polymer, the different structures can be understood as a step wise suppression of the Static Structure formation on the ramps. The stress component normal to the irradiated surface acts as an inhibitor of the Static Structure formation. At ramp angles lower than 10°, the structure on the ramps is identical to the structure on statically ablated surfaces. At 10° < θ < 30° the structure changes but is still present. At ramp angles higher than 30° the ramps are smooth. As the micrometric structure on the channel floor is given by the structure on the lower part of the irradiated ramp, the channel floor structure is of the same type as the structure on the ramp. However, it is not possible to obtain a smooth channel floor. The angle ranges for the different structures do not depend on the laser fluence but vary from one substrate material to another. The presence and the orientation of the micrometric structure only have negligible influence on the electroosmotic flow in the micro channels. In conclusion, the message of this work is that Scanning Ablation modifies drastically the ablated surface properties. This must be taken into account when thinking about fabricating devices for which properties such as wettability, adhesion, ζ-potential or micro/nano-roughness are important.