This work highlights the influence of layer thicknesses on glass transition and molecular mobility in polycarbonate (PC) and poly(ethylene terephthalate glycol) (PETg) multilayered films obtained by the layer-multiplying coextrusion process. By combining modulated temperature scanning calorimetry (MT-DSC) and dielectric relaxation spectroscopy (DRS) measurements, the average values of the cooperative rearranging region (CRR) size in a wide range of relaxation times and temperatures have been calculated. The size reduction from micro-to nanoscale is accompanied by a significant deviation of the structural and dynamical properties compared to the bulk. Furthermore, we have evidenced significant differences in PETg and PC behaviors: PETg plays the role of a "hard-confined" polymer, while PC behaves as a "free-confined" polymer, implying opposite variations of the glass transition temperature. The determination of the relaxation parameters for each individual polymer has been possible even for very low layer thicknesses (below 10 nm), for which the multilayer structure is not observed. This result shows that even when PETg and PC are brought into very intimate contact, they maintain their own structural behavior and segmental relaxation, suggesting the formation of immiscible nanodroplets when the multilayer structure disappears.