The influence of nanoscale out-of-plane roughness on the ordering of submicron spheres during evaporative deposition from colloidal suspension was examined using shallow corrugated substrates possessing optical wavelengths and nanoscale amplitude. Under conditions in which spheres were embedded in a liquid layer with thickness on the order of the sphere diameter, it was observed that the spheres overwhelmingly deposited in the valleys of the surface corrugations rather than on their peaks. This behavior persisted to surprisingly shallow corrugation amplitudes, sometimes 100 times smaller than the sphere diameter. An analysis of the capillary forces on the spheres explains this behavior and also yields a critical corrugation amplitude below which a substrate will appear "flat" to depositing spheres. The observation that substrate features significantly smaller than the sphere diameter can influence deposition morphology may lead to simple methods to create large domains of order in colloidal crystals.