Using a stainless shadow mask combined with a magnetron-ion-assisted deposition (IAD) sputtering system, we investigate the surface morphologies and optical properties of microfilms. Optimal color-filter (CF) coating microfilms with niobium pent-oxide (Nb2O5)/silicon dioxide (SiO2) multilayers on a hard polycarbonate (HPC) substrate, grown at 85 °C and 50 SCCM oxygen flow, can obtain a fairly uniform thickness (with an average roughness of 0.083 and 0.106 nm respectively for Nb2O5 and SiO2 films) through all positions. On a flexible HPC substrate with the Nb2O5/SiO2 microfilms, meanwhile, the peak transmittances measured in the visible range are 95.70% and 91.47%, respectively, for coatings with and without a shadow mask for this new-tech system. For the optimal CF application with a shadow mask, transmittance on each 100 nm band-pass wavelength is enhanced by 4.04% absolute (blue), 2.96% absolute (green), and 2.12% absolute (red). Moreover, the developed new-tech system not only enhances the quality of the films by achieving smoother and uniform surfaces but also reduces deposition time, thereby improving overall process efficiency. For the with-shadow-mask condition, there is little shift at 50% transmittance (T50%), and high transmittance (~97%) is maintained after high-temperature (200 °C) baking for 12 h. These results are well above the commercial CF standard (larger than 90%) and demonstrate reliability and good durability for flexible optical applications.