We used optical lithography, electroless deposition and deep reactive ion etching techniques to realize arrays of super-hydrophobic gold nanoparticles arranged in a hierarchical structure. At the micro-scale, silicon-micro pillars in the chip permit to manipulate and concentrate biological solutions, at the nano-scale, gold nanoparticles enable metal enhanced fluorescence (MEF) effects, whereby fluorescence signal of fluorophores in close proximity to a rough metal surface is amplified by orders of magnitude. Here, we demonstrated the device in the analysis of fluorescein derived gold-binding peptides (GBP-FITC). While super-hydrophobic schemes and MEF effects have been heretofore used in isolation, their integration in a platform may advance the current state of fluorescence-based sensing technology in medical diagnostics and biotechnology. This scheme may be employed in protein microarrays where the increased sensitivity of the device may enable the early detection of cancer biomarkers or other proteins of biomedical interest.