The morphology of the surface that you want functionalized do not change significantly because you are performing the growth of a molecular layer . The best way to confirm the functionalization is by using XPS or FTIR, that give you the relevant information about the establishment of new covalent bonds.
If you are coating any surface, it depends upon your surface morphology. Usually people employ different sensing platforms (SPR, QCM, electrodes) or characterization techniques such as XPS, ellipsometry, EIS, etc. to establish surface coating.
The morphology of the surface that you want functionalized do not change significantly because you are performing the growth of a molecular layer . The best way to confirm the functionalization is by using XPS or FTIR, that give you the relevant information about the establishment of new covalent bonds.