Surface reconstructions play a crucial role in surface science because of their influence on the adsorption and arrangement of molecules or nanoparticles. On the Au(111) surface, the herringbone reconstruction presents favorable anchoring at the elbow sites, where the highest reactivity is found. In this work, we deposited large organic perchlorinated molecules on a Au(111) surface via high-vacuum electrospray deposition. With noncontact atomic force microscopy measurements at room temperature, we studied the molecular structures formed on the surface before and after annealing at different temperatures. We found that a supramolecular layer is formed and that a hexagonal reconstruction of the Au(111) surface is induced. After hightemperature annealing, the molecules are removed, but the hexagonal Au(111) surface reconstruction is preserved. With the hexagonal Au(111) surface reconstruction, a periodic lattice of anchoring sites is formed.