Atomic depth profiling using secondary ion mass spectrometry, SIMS, is common in the field micro-electronics; however, the generation of molecular information as a function of sample depth is difficult due to the accumulation of damage both on and beneath the sample surface. The introduction of polyatomic ion beams such as SF5 and C60 have raised the possibility of overcoming this problem as they deposit the majority of their energy in the upper surface of the sample resulting in increased sputter yields but with a complimentary reduction in sub-surface damage accumulation. In this paper we report the depth profile analysis of the bio-polymer polycaprolactone, PCL, using the polyatomic ions Au3+ and C60+ and the monoatomic Au+. Results are compared to recent analysis of a similar sample using . depth profiling of cellulose is also demonstrated, an experiment that has been reported as unsuccessful when attempted with implications for biological analysis are discussed.