Throughout the materials community, there exists extensive literature on carbon fibre chemical, physical and mechanical properties, and the effect of these on composite performance. To date, however, the atomistic chemical nature of the changing carbon fibre surface when surface treatments are applied has been a very difficult area to study using experimental measurements alone. This study shows the potential of molecular simulation methods to be applied to real engineering materials, and the chemical insight that can be gained in using them. Inverse gas chromatography experiments show how the dispersive and acid-base nature of the carbon fibre surface changes as a function of surface treatment. In combination with these experimental measurements, the SORPTIOISFTM molecular modelling algorithm is used to develop models that provide a representation of the surfaces of these materials in terms of specific chemical functional groups. These models are compared with separate experimental data, and used to predict and describe aspects of the adhesion in the interfacial region of a carbon fibre-thermoset matrix resin composite.