Physico-chemical processes on the micro-scale require new modelling concepts because some effects become dominating that are negligible for macroscopic systems. This is illustrated by a new method for the production of micro-wells based on the placement of a small drop of toluene on a plate of polystyrene. After droplet evaporation, a micro-well is left. A mathematical model has been developed to understand the elementary processes of the micro-well formation. The model accounts for: (1) growth of the drop on the substrate, (2) evaporation process of the solvent, (3) dissolution of the substrate, (4) flow rate in the evaporating drop caused by the pinning effect, including the vertical velocity profile, and (5) increase in the concentration of dissolved material followed by precipitation. In the modelling and simulation process, it could be shown that the method of drop production also has a significant influence on the shape of the micro-wells.