Using scanning tunneling microscopy (STM), we followed the self-organization process of a supramolecular polymer monolayer deposited on a gold surface. During the growth of ordered domains from small to large scales, the molecule-molecule interactions were found to overrule the coupling to the substrate, causing a reorientation of the monolayer. The flexibility at the molecular level, due to reversible hydrogen bonds, was directly visualized by STM. The supramolecules were able to slide and insert between neighboring molecules, allowing the annihilation of domain boundaries and improving long range order. Large domains were found to cross monoatomic steps on the substrate without perturbation of their order.