The present thesis introduces the research of various fabrication strategies of bottom-up plasmonic nanostructures for the bio-analytical application. First, a novel label-free P. ramorum detection platform was realized employing SERS. This invasive plant pathogen was successfully detected and the entire analysis chain including, sample preparation, DNA isolation, amplification and hybridization on SERS-active silver substrate-immobilized adenine-free capture probes is introduced in the thesis. Later, the above introduced silver plasmonic arrays, so called EGNPs, were coated with the dielectric material Al2O3 using atomic layer deposition (ALD). These procedure increased their sensitivity, specificity and shelf-life. Second, hierarchically designed 3D flower-like hybrid nanostructures were developed by combining the metastable property of EGNPs substrates with plasma enhanced atomic layer deposition (PE-ALD). The resulting ultra-stable nanostructures were established as an efficient SERS-template substrate. Finally, an alternative silver nanoparticle synthesizing method using microwave radiation was proposed. This employs as a reliable, rapid, simple, reproducible and environmental friendly bottom-up fabrication strategy. The approach was implemented to the glass capillaries. An ultra-sensitive and high reproducible novel SERS-based capillary platform was developed and applied for the trace detection of THC. For this purpose, not only the physical, material and optical properties of these developed nanostructures were characterized but also their SERS efficiency was studied in detail. The developed novel SERS-active nanostructures show improved SERS performance in terms of high SERS reproducibility, surface uniformity, easy synthesis, cost-effectiveness, easy handling and high signal to noise ratio. Finally, the great potential of those novel SERS-active substrates in the field of biochemical and trace detection of an illegal drug were highlighted.