Nanostructured molecular thin films adsorbed on solid surfaces form the basis of numerous applications. Long-range order within adsorbed molecules is very often a desirable property for such systems. In this contribution, we report a simple and efficient method to fabricate well-aligned thin films of organic molecules over a few millimeter squares. The strategy involves use of capillary force in a two-step flow method to induce large-area alignment of multilayers of molecules at the organic liquid solid interface. Furthermore, we also demonstrate the influence of alignment on the electron transport through these well-aligned thin films using scanning tunneling spectroscopy.