Manufacturing technology designed to interface natural molecular components with a solid surface is fundamental in building higher-order complex functional structures from the nanoscale domain. Here, we present top-down fabrication approaches that define and guide the growth of natural molecular components, such as inorganic ions and proteins, and investigate how external control parameters can influence the growth of the resultant structures. Specifically, electron beam lithography was used to create nanoscale hydrophilic patterns on a hydrophobic substrate to entrap attoliter volumes of liquid containing inorganic ions. As these nanoscale droplets evaporated, they initiated the crystallization of the ions, resulting in the synthesis of nanoscale inorganic structures (∼50 nm - 300 nm). Through the use of scanning electron and atomic force microscopy, the effects of external control parameters, such as humidity and size of the hydrophilic patterns, to the formation of the resulting structures were quantified. In a separate but related effort, self-assembling actin filaments were grown from nanoscale binding sites created by electron beam lithography. High-aspect-ratio (∼ 1000:1) structures were demonstrated while maintaining the nanoscale surface geometries. These two technologies have laid down a foundation for the systematic study of these synthesized structures in artificial engineered environments.