This Account aims to describe our experience in the use of patterning techniques for addressing the self-organization processes of materials into spatially confined regions on technologically relevant surfaces. Functional properties of materials depend on their chemical structure, their assembly, and spatial distribution at the solid state; the combination of these factors determines their properties and their technological applications. In fact, by controlling the assembly processes and the spatial distribution of the resulting structures, functional materials can be guided to technological and specific applications. We considered the principal self-organizing processes, such as crystallization, dewetting and phase segregation. Usually, these phenomena produce defective molecular films, compromising their use in many technological applications. This issue can be overcome by using patterning techniques, which induce molecules to self-organize into well-defined patterned structures, by means of spatial confinement. In particular, we focus our attention on the confinement effect achieved by stamp-assisted deposition for controlling size, density, and positions of material assemblies, giving them new chemical/physical functionalities. We review the methods and principles of the stamp-assisted spatial confinement and we discuss how they can be advantageously exploited to control crystalline order/orientation, dewetting phenomena, and spontaneous phase segregation. Moreover, we highlight how physical/chemical properties of soluble functional materials can be driven in constructive ways, by integrating them into operating technological devices.