In this work, the formation of laser-induced periodic surface structures (LIPSS) on the surfaces of thin films of poly(ethylene terephthalate) (PET) and PET reinforced with expanded graphite (EG) was studied. Laser irradiation was carried out by ultraviolet (265 nm) and near-infrared (795 nm) femtosecond laser pulses, and LIPSS were formed in both materials. In all cases, LIPSS had a period close to the irradiation wavelength and were formed parallel to the polarization of the laser beam, although, in the case of UV irradiation, differences in the formation range were observed due to the different thermal properties of the neat polymer in comparison to the composite. To monitor the modification of the physicochemical properties of the surfaces after irradiation as a function of the laser wavelength and of the presence of the filler, different techniques were used. Contact angle measurements were carried out using different reference liquids to measure the wettability and the solid surface free energies. The initially hydrophilic surfaces became more hydrophilic after ultraviolet irradiation, while they evolved to become hydrophobic under near-infrared laser irradiation. The values of the surface free energy components showed changes after nanostructuring, mainly in the polar component. Additionally, for UV-irradiated surfaces, adhesion, determined by the colloidal probe technique, increased, while, for NIR irradiation, adhesion decreased. Finally, nanomechanical properties were measured by the PeakForce Quantitative Nanomechanical Mapping method, obtaining maps of elastic modulus, adhesion, and deformation. The results showed an increase in the elastic modulus in the PET/EG, confirming the reinforcing action of the EG in the polymer matrix. Additionally, an increase in the elastic modulus was observed after LIPSS formation.