Molecular transport processes in printed polymer droplets hold enormous importance for understanding wetting phenomena and designing systems in applications such as encoding, electronics, photonics, and sensing. This paper studies thickness‐dependent dewetting modes that are activated by thermal annealing and driven by interfacial interactions within microscopically confined polymeric features. The printing of poly(2‐vinylpyridine) is performed in a regime where coffee‐ring effects lead to strong thinning of the central region of the deposit. Thermal annealing leads to two different modes of dewetting that depend on the thickness of the central region. Mode I refers to the formation of randomly positioned small features surrounded by large hemispherical ones located along the periphery of the printed features and occurs when the central regions are thin. Observed at large central thicknesses, Mode II mediates significant molecular transport from edges toward the center of the printed droplet with thermal annealing and forms a hemispherical feature from the initial ring‐like deposit. The selective adsorption of red, green, and blue emitting quantum dots over the poly(2‐vinylpyridine) results in photoluminescent patterns. The selective assembly of photoluminescent quantum dots over patterned surfaces leads to deterministic and stochastic features beneficial to creating security labels for anti‐counterfeiting applications.