Patterned organosilane self-assembled monolayers serve as molecular platforms for electronic, optical, and sensing applications. Among the numerous strategies to pattern organosilane monolayers, particle lithography offers a high throughput means to fabricate arrays of organosilane nanopatterns across large areas. Herein, we demonstrate that the utility of particle lithography for generating nanostructures can be further controlled by changes in sample preparation. Our systematic study of various drying conditions demonstrates a correlation between sample preparation and surface water and uses these findings to form nanopores, pillars, and rings within organosilane monolayers. Silica mesospheres deposited on Si substrates that are subjected to less rigorous drying conditions (3h at room temperature) prior to organosilane deposition yield nanopores within decyltrichlorosilane monolayers that are significantly smaller than those produced on Si substrates that are prepared under more forcing conditions (12 h at room temperature and 2 h at 140 degrees C). This disparity in nanopore diameter can be rationalized by the presence or absence of water between the silica mesospheres and Si substrate. Sequential deposition of two organosilanes offers further evidence for the presence or absence of water beneath the silica mesospheres. For samples that are less rigorously dried, complete organosilane pillars are observed, and for samples that are more rigorously dried, organosilane rings are observed where the inner diameter is defined by the mesosphere-substrate contact geometry. The ability to produce varied organosilane nanostructures provides valuable insights about the water that is present on the surface and within the silica mesosphere template. These insights into the surface water and the effects of sample preparation on organosilane nanostructures enable greater hierarchical control over the fabrication process. (C) 2015 Elsevier B.V. All rights reserved.