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The present work describes a methodology for patterning biomolecules on silicon analytical devices, such as novel Bio-MEMS or conventional biosensors, that reconciles three-dimensional (3-D) biological functionalisation with standard resist lift-off techniques. Unlike classic sol-gel approaches in which the biomolecule of interest is introduced within the sol mixture, a two-stage scenario has been developed. It consists firstly of patterning micron scale polycondensate scaffold structures - using classic microfabrication tools - which are then loaded with native biomolecules via a second simple incubation step under biologically-friendly environmental conditions. The common compatibility issue between the biological and microfabrication worlds has been circumvented since native recognition biomolecules can be introduced into the host scaffolds downstream of all compatibility issues. The scaffolds can be generated on any silicon substrate via polycondensation of aminosilane - namely aminopropyltriethoxy silane (APTES) - under conditions that are fully compatible with resist mask lithography. The scaffold porosity and high primary amine content allow proteins and nucleic acid sequences to penetrate the polycondensate and to interact strongly, thus giving rise to micron/sub-micron 3-D structures exhibiting high biological activity. The integration of such a bio-patterning approach in the microfabrication process of analytical devices has been demonstrated via the successful biofunctionalisation with recognition antibodies and/or nucleic acid sequences of MEMS circular diaphragm resonator (CDR) sensor patterns.