Scanning tunnelling microscopy (STM) experiments at protein–semiconductor systems are analyzed using concepts from applied semiconductor physics such as Fermi level pinning and MIS (metal–insulator–semiconductor) junction electronics. Routes for immobilization of enzymes (proteins) on nanostructured surfaces of MoTe2 and Si are outlined using so‐called DLVO and non‐DLVO interaction forces. An overview of the catalytic activity of the imaged enzymes, reverse transcriptases of the retroviruses HIV 1 and AMV (avian myeloblastosis virus), is given including their tertiary structural properties which is revealed also in the STM and tapping mode AFM images. For the interpretation of STM images, a resonant charge transfer mechanism is invoked, based on the potential dependence of the image contrast and the energy band structure of MoTe2 near the valence band maximum. First analyses of the charge transport from the semiconductor to the STM tip at negative bias of MoTe2 suggest that the observed uninhibited conductivity in the constant current experiments results from solvation‐assisted release of electrons from traps that exist along the polypeptide chains and that charge transport occurs at the circumference of the enzymes where biological water is present. Therefore, charge injection into catalytically active enzymes such as hydrogenase or water oxidase of Photosystem I and II with subsequent charge transport to the active sites appears difficult to realize. Possibilities of radiation‐less long‐distance energy transfer based on the Förster mechanism, its multichromic extension and on Dexter exciton hopping are considered for catalytically active hybrid inorganic/organic absorber–enzyme structures. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)