Scanning tunneling microscopy is used to monitor the influence of a controlled nanometer scale surface roughness on structure and stability of physisorbed, crystallized monolayers at the interface between graphite and molecular solutions. The basal plane of graphite is modified by creating atomic scale defects, which are subsequently thermally oxidized to yield monolayer deep circular pits of controlled two-dimensional density and diameters. Alkanes and alkylated oligothiophenes are adsorbed as flat-lying lamellae from solution. Monolayer crystallization is inhibited when the mean distance between the pits becomes comparable to the size of a single molecule. On a time scale of 100 ms, the critical pit diameter for the formation of ordered domains within a pit is two to three lamella widths (6-8 nm). These domains are stabilized and decoupled from those on the terrace. When the pit diameter is increased by a factor of 8 -10, the stability inside the pit can be increased by 4 orders of magnitude. This means that the information connected to the orientation of the lamellae of a domain can be stored on time scale of 100 ms in as little as about a dozen molecules.