Carbohydrate-binding modules (CBMs) are a set of tools that can be used as molecular probes for studying plant cell walls and cellulose-based substrates. CBMs from enzymes of bacterial and fungal origin present a range of recognition capabilities for crystalline and amorphous cellulose. Here cellulose-directed CBMs have been used to visualize and quantify crystallinity changes in cellulose II-based polymers following NaOH treatment. Cellulose II polymers used were in the form of lyocell fibers, which are derived from eucalyptus wood pulp. The supramolecular structure, morphology, and existence of ‘skin-core’ model in the fiber were examined using CBM-labeling techniques. Changes in cellulose crystallinity showed maxima at 3.33 mol dm−3 NaOH (under treatment conditions of 49 N m−1 at 25 °C) and 4.48 mol dm−3 NaOH (under treatment conditions of 147 N m−1 at 40 °C); CBM methods were also suitable for quantifying changes within amorphous regions. Quantification of crystallinity changes using CBM labeling techniques was achieved in combination with image analysis, which was shown to reflect the same crystallinity changes as measured using ATR-FTIR methods. It was demonstrated that CBM-labeling techniques were able to validate the proposed ‘skin-core’ model of lyocell fibers, comprising a semi-permeable fiber skin and a porous core.