We demonstrate a method for the simultaneous fabrication (without the need of expensive e-beam systems) of large arrays of nanodevices working at room temperature. The electrode gap is defined by a selective wet-etching of a AlGaAs/GaAs quantum well structure and controlled with nanometer precision. A selective oxidation of the Al rich barrier reduces the bulk leakage current by six orders of magnitude and extends the applicability of the produced devices to room temperature functionality. As a demonstration, we employ here these nanojunctions to investigate transport in molecular tunnel-junctions based on individual Azurins, a blue copper protein, under ambient conditions. This approach opens the way to the fabrication of complex circuits consisting of different nanodevices.