Agarose based hydrogels doped with amino-propyl-triethoxy-silane have been prepared and used for the biofunctionalization of hydroxylated Si (100) surfaces. The doped hydrogels consist of two independent polysaccharide and siloxane networks. The confluent colloidal layer coverage of the substrate from the transferring hydrogels is illustrated by various techniques. The line shape of the N 1s and C 1s X-ray photoemission spectra is shown to depend strongly on the polar angle of the photoelectron emission. This effect is explained in terms of different indepth distributions of N and C species and the dominant presence of surface oriented amino groups. The surface modification induces an alteration of wettability, but the intrinsic nanoscale topography of the transferred films is the determinant factor of the interaction with water. Furthermore, it is found that the transferred functionalization is compatible with the formation of sub-micrometer patterns by exploiting as masks polystyrene based colloidal monolayers. Both nanodots and nanoporous wells with a hexagonal lattice were observed by atomic force microscopy and their biofunctionality demonstrated by fluorescence microscopy after fluorophore labelled IgG immobilization.