Surface functionalization of 1D materials such as silicon nanowires is a critical preparation technology for biochemical sensing. However, existing nonselective functionalization techniques result in nonlocal binding and contamination, with potential device damage risks. Associated risks are further exacerbated for next-generation devices of a 3D nature with challenging topographies. Such 3D devices draw inspiration from the out-of-plane evolution of planar transistors to FinFETs and to today's gate-all-around transistors. This study is the first reported technological work addressing stencil-based surface decoration and selective functionalization of a suspended silicon nanowire building block embedded within such a device that involves two-order-of-magnitude thicker features compared to the nanowire critical dimensions. A gold pattern resolution of 3.0 mu m atop the silicon nanowires is achieved with a stencil aperture critical dimension of 2.2 mu m, accompanied by a die-level registration accuracy of 1.2 +/- 0.3 mu m. Plasma-enhanced chemical vapor deposition-based silicon nitride stencil membranes as large as 300 x 300 mu m2 are used to define the apertures without any membrane fracture during fabrication and membrane cleaning. The pattern-blurring aspect as a resolution-limiting factor is assessed by using 24 individual nanowire devices. Finally, gold-patterned silicon nanowires are functionalized using thiolated heparin and employed for selective attachment and detection of the human recombinant basic fibroblast growth factor (FGF-2). With the potential involvement in angiogenesis, the process of new blood vessel formation crucial for tumor growth, FGF-2 can serve as a potential prognostic biomarker in oncology. Demonstrated selectively on nanowires with high pattern resolution, the proposed functionalization approach offers possibilities for parallel sensing using vast nanowire arrays embedded in 3D device architectures developed for next-generation biochemical sensors in addition to serving various encapsulation and packaging needs.