The inherent colloidal dispersity (due to length, aspect ratio, surface charge heterogeneity) of CNCs, when produced using the typical traditional sulfuric acid hydrolysis route, presents a great challenge when interpreting colloidal properties and linking the CNC film nanostructure to the helicoidal self-assembly mechanism during drying. Indeed, further improvement of this CNC preparation route is required to yield films with better control over the CNC pitch and optical properties. Here we present a modified CNC-preparation protocol, by fractionating and harvesting CNCs with different average surface charges, rod lengths, aspect ratios, already during the centrifugation steps after hydrolysis. This enables faster CNC fractionation, because it is performed in a high ionic strength aqueous medium. By comparing dry films from the three CNC fractions, discrepancies in the CNC self-assembly and structural colors were clearly observed. Conclusively, we demonstrate a fast protocol to harvest different populations of CNCs, that enable tailored refinement of structural colors in CNC films.