Chemically passivated gold nanoclusters deposited on the surface of graphite have been manipulated with the scanning tunneling microscope (STM) in ultrahigh vacuum. The controlled clearing of a definite shape in a cluster layer is demonstrated. Clusters embedded in a close-packed array could not be removed from the surface, apparently because of the attractive interaction between neighboring ligand chains. A minority channel of cluster fragmentation has been identified and leads to the creation of platelets which can be further manipulated by the STM tip. ©1998 American Institute of Physics.