We report on the nanostructures of organic small-molecule pentacene crystals that have been vapor-deposited onto the capillary wave surfaces of thin liquid films. The characteristic lateral length of the capillary wave surface or the capillary length can be controlled by changing the thickness of the liquid films and, thus, the van der Waals interaction with the substrate. We find that the morphology of the organic crystals gradually varies from fractals to compact islands as the liquid film thickness increases. The square of average distance between organic crystal grains was also found to be proportional to the liquid film thickness. We discuss the possibility that these effects are driven by capillary fluctuations at the air-liquid interface.