Femtosecond laser ablation is a promising method for producing polymeric microfluidic devices: it is a high precision processing technology resulting from an efficient energy deposition, while simultaneously minimizing heat conduction and thermal damage to the surrounding material. This work reports on the characterization of microchannels and waveguides fabricated by femtosecond laser technology in methacrylate-based polymers, precisely in thermoplastic poly(methyl methacrylate) (PMMA) and in a new material based on a high efficiency UV-curing process of methacrylic monomers bearing hydrophilic polyethylene glycol chains, namely tetraethylene glycol dimethacrylate and poly(ethylene glycol) methacrylate (PEG-MA). Microchannels in PMMA and PEG-MA, fabricated by parallel multi-scans, have sharp edges and low roughness, as investigated by Environmental Scanning Electron Microscopy and laser profilometer. Surface and physico-chemical properties after fs-laser processing were further studied by contact angle measurements and Attenuated Total Reflectance FTIR spectroscopy. Moreover, preliminary tests showed the refractive index of fs-laser PEG-MA exposed zones is different with respect to that of the surrounding polymer, suggesting that PEG-MA can be a good candidate to manufacture microfluidic devices containing integrated optic elements.