Soft organic surfaces with more and more complex topologies are required daily to engineer appropriate microstructures for many different applications such as DNA array technology, biological optics for advanced photonic systems and microfluidics. Complementarily to conventional lithographic processes, several pioneering methods have been developed recently, by controlling phase separation of polymer blends, spinodal decomposition of homopolymers or by using the action of additional external forces driving diverse instabilities. Here we present a method that not only provides original concepts towards the three-dimensional (3D) structuring of liquids, on the basis of the synergistic effects of molecular diffusion and confined nucleation, but also suggests original solutions for the transport, mixing and filtering of small volumes of liquid. Through the intrinsic destabilization of a liquid-liquid bilayer, the 2D pattern of a chemically structured surface with 'hydrophilic' and 'hydrophobic' domains is transferred to a solid/liquid interface as a 3D topography with either 'positive' or 'negative' replication. This easy-to-use process has potential applications in various technological realms requiring a specific topography at interfaces such as microfluidics or biosensors.