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Recently, solvent exchange has been demonstrated as a simple solution-based approach for the controlled formation of surface nanodroplets over large areas. The as-formed surface nanodroplets provide new opportunities for a wide range of droplet-based applications. Herein, it is demonstrated that surface nanodroplets can be used as versatile structural templates for the fabrication of functional surfaces with tailored wettability and morphology. Guided by the microstructural and wetting properties of desert beetle’s back and cactus spine, two types of functional surfaces have been prepared. The first biomimetic surface of desert beetle’s back, with hydrophilic lumps on a hydrophobic background, was obtained by independent selective surface modification of polymerized surface nanodroplets and the background surface. The second surface, with anisotropic wetting microstructures, was fabricated by controlled deposition of droplets on the rim of polymer lenses. The results showed systematic improvement of wettability and efficiency of water collection by using the as-prepared biomimetic surfaces, compared with substrates without the designed microstructures. This work demonstrates surface nanodroplets as a new type of template in the design and preparation of functional surfaces with controlled wettability and morphology.