Metallic nanostructures and their fabrication methods have been studied for over decades as they are crucial in developing plasmonic sensing platforms. In this work, a hierarchical nanopillar huddle structure fabricated by thermal nanoimprint lithography with anodic porous alumina as template is presented. By utilizing this scheme, nanopillars (branches) rooted on regularly deployed substructures (footings) can be easily produced/reproduced for large working area at low-cost with high-throughput. After metal deposition for plasmon activation, tiny nanogaps were generated within each single huddle. The as-fabricated substrates are also tunable by varying the anodizing conditions and metal deposition material/thickness. Substrates produced using this scheme were evaluated by absorption spectra measurements and SERS detection of series of adsorbed molecules. Finite-difference time-domain (FDTD) simulation was conducted to validate the promising feature of the higher electric field energy density stimulated at the tiny nanogaps which resulted in a regular distribution of "hot-spots". Finally, biosensing potentials were demonstrated by conducting measurements of four different nucleotides (i.e. AMP, CMP, TMP, GMP at 10 −2 M) using silver sputtered substrate without any modification. Its SERS performance in the micron level was also evaluated via line-scan in two orthogonal direction in 10 −2 M AMP solution.