Nanopatterned microneedle (MN) has garnered significant attention for its potential to modulate surface characteristics, particularly in applications such as drug delivery, biosensing, and transdermal diagnostics. However, achieving precise nanopatterning on 3D polymeric surfaces of MN array while maintaining the structural and functional stability of the material remains a challenge. In this study, we describe a method for fabricating 3D nanopatterns on MN surfaces using a directionally controlled plasma etching technique. By adjusting the plasma incidence angle during etching, distinct 3D patterns, including nanogroove geometries, were successfully produced. The pattern morphology was systematically investigated through variations in parameters such as chuck bias power and incidence angle. To enable selective etching, an etch mask composed of gold nanoparticles (AuNPs) encapsulated in polystyrene–poly(acrylic acid) (PS–PAA) block copolymer micelles was employed. A polyelectrolyte multilayer, formed by alternate deposition of cationic poly(allylamine hydrochloride) (PAH) and anionic poly(styrenesulfonate) (PSS), provided strong electrostatic anchoring for the AuNP@PS–PAA micelles. This system served as an effective etch mask, protecting the underlying polymer surface from plasma etching in the regions where the micelles were adsorbed. The resulting nanopatterns significantly modified surface topography without degrading the mechanical properties of MN. Specifically, insertion force into porcine skin remained comparable to the nonpatterned MN, indicating that the introduction of 3D nanopatterns does not impair the material’s primary mechanical function. Furthermore, nanopatterned MN exhibited a notable enhancement in adhesion, with up to a 6-fold increase compared to nonpatterned MN. This was attributed to the increased surface area and additional contact interfaces created by the patterns, facilitating stronger interactions with biological substrates. This work demonstrates that precise 3D nanopatterning via plasma etching can effectively tailor surface properties while preserving the functional integrity of polymeric biomaterials, offering broad applicability in biomedical engineering.