We have developed a procedure for atomic scale alignment with respect to macroscopic objects. Metallic and etched registration marks on clean reconstructed Si surfaces are used to guide the tip of a scanning tunnelling microscope. The metallic marks are formed from Ta and can withstand thermal cycling up to 1500 K. These procedures have been used to investigate the interaction of Ag with a patterned fullerene multilayer deposited on Si(111)-7×7.©1997 American Institute of Physics.