<p>Aerosol deposition (AD) is capable of producing dense nanocrystalline ceramic films at room temperature. Most studies have focused on flat, smooth substrates, but the growing demand for miniature devices requires coatings on various substrates, including rough, structured, or patterned surfaces. This study investigates the influence of substrate structures in AD by depositing alumina coatings on patterned silicon (Si) substrates. The growth process and microstructure of coatings deposited on Si substrates with different pillar widths, heights, and spacings have been analyzed. Results show that coatings initially form in the valleys with particle fragments before covering the entire pattern and developing a uniform layer. We demonstrate that the relative size of the substrate patterns and powder particles significantly influences the coating microstructure, particularly in the valleys between the pillars. Dense coatings were deposited on all patterned substrates except those with deep, narrow valleys, where only accumulated powders were found in the grooves.</p>