The irreversible (6x6) reconstruction of the C(60)/Al(111) system from the (2sqrt[3]x2sqrt[3])R30 degrees phase is studied by first-principles techniques. We find that C60 binds optimally to the surface if an Al vacancy is created directly underneath. The removed Al atoms form a (6x6) array of ad-dimers in the interstices below the C60 overlayer, to which they strongly bind. This spontaneous local process, rather than the compression state of the unreconstructed C60 overlayer, explains why one molecule out of three protrudes from the surface upon reconstruction.