Different nanotechnological strategies have been designed to implement the production of innovative diagnostic and optical sensing devices for genomic and proteomic applications. In this chapter, we will give an overview on the novel nanobiotechnological approaches recently developed, combining top-down nanostructuring and bottom-up molecular self-assembly to soft lithography, with molecular biology tools, aimed at the production of high-performance plastic chips for diagnostics and nanostructured materials to be applied in advanced sensing and imaging. Highly sensitive fluorescence imaging/sensing schemes, enabling the enhancement of sensors sensitivity and detection limits, such as Metal Enhanced Fluorescence- and Photonic Crystals-based approaches, will be discussed as novel tools for the detection of biological targets (e.g., DNA, proteins, and fibrils).