This study reports an experimental validation of the surface preferential nucleation of proteins on the basis of a relationship between nucleant pore diameter and protein hydrodynamic diameter. The validated correlation was employed for the selection of nucleant pore diameter to crystallise a target protein from binary, equivolume protein mixture. We report proof-of-concept preliminary experimental evidence for the rational approach for crystallisation of a target protein from a binary protein mixture on the surface of 3D nanotemplates with controlled surface porosity and narrow pore-size distribution selected on the basis of a relationship between the nucleant pore diameter and protein hydrodynamic diameter. The outcome of this study opens up an exciting opportunity for exploring protein crystallisation as a potential route for protein purification and bio-separation in both technical and pharmaceutical applications.