Plasmonic nanoparticle clusters promise to support various, unique artificial electromagnetisms at optical frequencies, realizing new concept devices for diverse nanophotonic applications. However, the technological challenges associated with the fabrication of plasmonic clusters with programmed geometry and composition remain unresolved. Here, we present a freeform fabrication of hierarchical plasmonic clusters (HPCs) based on omnidirectional guiding of evaporative self-assembly of gold nanoparticles (AuNPs) with the aid of 3D printing. Our method offers a facile, universal route to shape the multiscale features of HPCs in three-dimensions, leading to versatile manipulation of both far-field and near-field characteristics. Various functional nanomaterials can be effectively coupled to plasmonic modes of the HPCs by simply mixing with AuNP ink. We demonstrate in particular an ultracompact surface-enhanced Raman spectroscopy (SERS) platform to detect M13 viruses and their mutations from femtolitre volume, sub-100pM analytes. This SERS microplatform could pave the way towards simple, innovative detection methods of diverse pathogens, which is in high demand for handling pandemic situations. We expect our method to freely design and realize nanophotonic structures beyond the restrictions of traditional fabrication processes. Plasmonic nanoparticle clusters have attracted great attention due to the unique capability to manipulate electromagnetic fields at the sub-wavelength scale1–5. Ensembles of metallic nanoparticles generate various electromagnetisms at optical frequencies such as artificial magnetism6–10 and Fano-like interference11–13 and a strong field localization in the structure14–16. These unique properties are geometry-dependent and lead to a broad range of applications in sensing16,17, surface-enhanced spectroscopies18–22, nonlinear integrated photonics23,24, and light harvesting25,26. Traditionally, plasmonic clusters with tailored size and geometry are fabricated on substrates by top-down processes such as electron-beam lithography4,5 or focused-ion beam milling27,28. These approaches suffer from low throughput and are generally limited to in-plane fabrication. Alternatively, the self-assembly of colloids has been proposed as a versatile, high-throughput, and cost-effective route. A number of clever methods based on chemical linking (e.g., DNA origami)29–30 and/or convective assembly on lithographically structured templates25,26,31 have been devised to construct 2D or 3D plasmonic clusters. The shape formation, however, is mostly constrained by the thermodynamic impetus and/or template geometry. A significant challenge would be overcome these restrictions and expand structural design freedom in the fabrication of plasmonic cluster architectures with symmetry-breaking geometries. In this work, we develop a freeform, programmable 3D assembly of of hierarchical plasmonic clusters (HPCs). By exploiting micronozzle 3D printing, we demonstrate highly localized, omnidirectional meniscus-guided assembly of metallic nanoparticles, constructing a freestanding HPC with a tailored geometry that can control the far-field character. Our approach also allows versatile manipulation and exploitation of the near-field interaction in the HPC by a facile heterogeneous nanoparticle mixing. We demonstrate that 3D-printed HPCs can be utilized as an ultracompact surface-enhanced Raman spectroscopy (SERS) platform to detect M13 viruses and their mutations from femtolitre volume, sub-100pM analytes.