[en] The effects of hyperthermal proton bombardment on alkanethiol self-assembled monolayer (SAM) on Au(1 1 1) are studied with scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS). The STM and XPS results show that proton bombardment with proton energy as low as 2 eV can induce cross-linking of the adsorbed alkanethiols and transform the original ordered SAM lattice to an array of nanoclusters of the cross-linked alkanethiols. For a bombardment at 3 eV with a fluence of 3x10¹⁵ cm^-2, the typical cluster size is about 5 nm. In addition, the cluster size distribution is narrow, with no cluster larger than 8 nm. The cluster growth can be promoted by increasing the fluence at a fixed bombardment energy or increasing the energy at a fixed fluence. This indicates that surface diffusion of alkanethiols and cluster growth can be harnessed by the control of the bombardment energy and fluence