Using variable temperature scanning tunnelling microscopy (STM), we studied the ordering processes on thiol-covered Au(111) surfaces at both the mesoscopic and microscopic scale. Because of the chemical erosion accompanying the self-assembly process, thiol-covered gold surfaces present small depressions, a few nanometres in size and one gold layer in depth. These defects can be healed by heating the monolayer up to 350-370 K. By performing isothermal STM measurements at elevated temperature (320-360 K), we followed the growth kinetics of the holes. The vacancy islands are found to coarsen by an Ostwald ripening mechanism, The molecular ordering of the thiol monolayers was also studied. The coexistence of several stable molecular conformations at room temperature was revealed. The well-ordered molecular domains extend over 100-200 Angstrom. The dominant domain configurations contain two superstructures with four molecules per unit cell. The origin of the STM image contrast is discussed.