The role of the location of energy deposition during cluster ion bombardment on the quality of molecular depth profiling was examined by varying the incident angle geometry. Cholesterol films approximately 300 nm in thickness deposited onto silicon substrates were eroded using 40-keV C60(+) at incident angles ranging from 5 degrees to 73 degrees with respect to the surface normal. The erosion process was evaluated by determining at each incident angle the total sputtering yield of cholesterol molecules, the damage cross section of the cholesterol molecules, the altered layer thickness within the solid, the sputter yield decay in the quasi-steady-state sputter regime, and the interface width between the cholesterol film and the silicon substrate. The results show that the total sputtering yield is largest relative to the product of the damage cross section and the altered layer thickness at 73 degrees incidence, suggesting that the amount of chemical damage accumulated is least when glancing incident geometries are used. Moreover, the signal decay in the quasi-steady-state sputter regime is observed to be smallest at off-normal and glancing incident geometries. To elucidate the signal decay at near-normal incidence, an extension to an erosion model is introduced in which a fluence-dependent decay in sputter yield is incorporated for the quasi-steady-state regime. Last, interface width calculations indicate that at glancing incidence the damaged depth within the solid is smallest. Collectively, the measurements suggest that decreased chemical damage is not necessarily dependent upon an increased sputter yield or a decreased damage cross section but instead dependent upon depositing the incident energy nearer the solid surface resulting in a smaller altered layer thickness. Hence, glancing incident angles are best suited for maintaining chemical information during molecular depth profiling using 40-keV C60(+).