This study aims to advance the understanding of pulp fibre properties by integrating advanced characterisation techniques, such as secondary ion mass spectrometry (SIMS) and x-ray scattering (WAXS/SAXS), with conventional fibre and paper evaluation methods. By combining traditional fibre characterisation with spatially resolved insights into the distribution of lignin, hemicellulose, and cellulose from SIMS and fibre wall morphology from X-ray analysis, this research provides a comprehensive understanding of the factors influencing the final properties of paper. The study focuses on chemical and morphologically distinct fibres, such as bleached kraft pulp (NBSK) and chemi-thermomechanical pulp (CTMP), processed under varying refining conditions. Our initial study shows a surface molecular analysis of NBSK paper highlighting the lignin and galactoglucomannan (Figure 1a) and the distribution of oxygen, carbon-nitrogen and sulfur ions (Figure 1b). A multi-technique approach is employed, utilizing high-resolution SIMS imaging with gas cluster ion beam (GCIB) technology for molecular mapping, alongside water retention value, zero-span tensile testing, and molecular weight analysis to assess fibre quality. Additionally, x-ray scattering techniques offer insights into fibre morphology and crystallinity. Refining experiments and fibre analyses are conducted at multiple PFI mill treatment levels to ensure a detailed investigation of fibre modifications. The findings contribute to fibre characterisation and sustainable materials, facilitating the precise modification and optimisation of fibre properties for industrial applications, new insights into how fibre composition and nanostructure affect paper strength and formability and the establishment of a unique database of chemical and morphological properties of NBSK and CTMP fibres, benefiting academic and industrial stakeholders.