Polyalanine molecules (PA) with an α-helix conformation gathered recently a lot of interest as the propagation of electrons through the chiral backbone structure comes along with spin polarization of the transmitted electrons. By means of scanning tunneling microscopy and spectroscopy at ambient conditions, PA molecules adsorbed on surfaces of epitaxial magnetic Al 2 O 3 /Pt/Au/Co/Au nanostructures with perpendicular anisotropy were studied. Thereby, a correlation between the PA molecules ordering at the surface with the electron tunneling across this hybrid system as a function of the substrate magnetization orientation as well as the coverage density and helicity of the was observed. The highest spin polarization values, P, were found for well-ordered self-assembled monolayers and with a defined chemical coupling of the molecules to the magnetic substrate surface, showing that the current induced spin selectivity is a cooperative effect. Thereby, P deduced from the electron transmission along unoccupied molecular orbitals of the helical molecules is larger as compared to values derived from the occupied molecular orbitals. Apparently, the larger orbital overlap is resulting in a higher electron mobility yielding a higher P value. By switching the magnetization direction of the Co-layer, it was demonstrated that the non-spin-polarized STM can be used to study chiral molecules with a sub-molecular resolution, to detect properties of buried magnetic layers and to detect the spin polarization of the molecules from the change of the magnetoresistance of such hybrid structures.