From anti-counterfeiting to biotechnology applications, there is a strong demand for encoded surfaces with multiple security layers that are prepared by stochastic processes and are adaptable to deterministic fabrication approaches. Here, we present dewetting instabilities in nanoscopic (thickness <100 nm) polymer films as a form of physically unclonable function (PUF). The inherent randomness involved in the dewetting process presents a highly suitable platform for fabricating unclonable surfaces. The thermal annealing-induced dewetting of poly(2-vinyl pyridine) (P2VP) on polystyrene-grafted substrates enables fabrication of randomly positioned functional features that are separated at a microscopic length scale, a requirement set by optical authentication systems. At a first level, PUFs can be simply and readily verified via reflection of visible light. Area-specific electrostatic interactions between P2VP and citrate-stabilized gold nanoparticles allow for fabrication of plasmonic PUFs. The strong surface-enhanced Raman scattering by plasmonic nanoparticles together with incorporation of taggants facilitates a molecular vibration-based security layer. The patterning of P2VP films presents opportunities for fabricating hybrid security labels, which can be resolved through both stochastic and deterministic pathways. The adaptability to a broad range of nanoscale materials, simplicity, versatility, compatibility with conventional fabrication approaches, and high levels of stability offer key opportunities in encoding applications.