Nanopatterned microneedles (MNs) have garnered attention for modulating surface characteristics in drug delivery and biosensing applications. However, achieving precise nanopatterning on 3D polymeric MNs while maintaining structural stability remains a challenge. We report a method for fabricating 3D nanopatterns on MN surfaces using directionally controlled plasma etching. Gold nanoparticle-encapsulated micelles, anchored via electrostatic layer-by-layer deposition, served as etch masks for complex geometries. The resulting nanopatterns modified surface topography without compromising mechanical properties. Insertion force into porcine skin remained comparable to non-patterned MNs, indicating preserved functional integrity. Furthermore, nanopatterned MNs exhibited a six-fold increase in tissue adhesion compared to controls due to increased contact interfaces. This precise 3D nanopatterning strategy effectively tailors surface properties, offering broad applicability in biomedical engineering.