Time-of-flight secondary ion mass spectrometry is utilized to characterize the response of Langmuir-Blodgett (LB) multilayers under the bombardment by buckminsterfullerene primary ions. The LB multilayers are formed by barium arachidate and barium dimyristoyl phosphatidate on a Si substrate. The unique sputtering properties of the C60 ion beam result in successful molecular depth profiling of both the single component and multilayers of alternating chemical composition. At cryogenic (liquid nitrogen) temperatures, the high mass signals of both molecules remain stable under sputtering, while at room temperature, they gradually decrease with primary ion dose. The low temperature also leads to a higher average sputter yield of molecules. Depth resolution varies from 20 to 50 nm and can be reduced further by lowering the primary ion energy or by using glancing angles of incidence of the primary ion beam.