In this article, we present an overview and prospective of inhomogeneous thin deposits of functional materials, which are usually unusable for applications as deposited. We show how common unwanted morphologies, such as crystallites, dewetting and fibrils can be transformed by driving their self-organization with external tools. In the first part we consider self-organization leading to thin deposits from compounds molecularly dispersed in a solution focusing on the relationship between the microscopic morphology appearing upon aggregation onto surfaces and the functional properties of these materials. In particular we considered the formation of crystallites, fibrils and droplets. In the second part we show how the inhomogeneous (and often unwanted) morphologies can be "corrected" by unconventional lithography in their self-organization becoming functional for several devices.