Surface adsorption of
C
60
affects its chemical and electronic properties. Numerous studies have reported observation of bright and dark fullerenes on metal surfaces that suggest extensive surface reconstruction; however, the underpinning mechanism of the reconstruction remains under debate. Here we report tip-functionalized noncontact atomic force microscope measurements which unambiguously reveal that
C
60
fullerenes adsorb with three well-defined adsorption heights on the Cu(111) surface, consistent with theoretical reports of top-layer hollow sites, single-atom vacancies, and surface nanopits. Using single-molecule resolution
Δ
f
(
z
)
measurements we identify well-defined adsorption heights specific to each site, confirming the presence of a complex vacancy model for
C
60
monolayers on metal surfaces.