This paper presents a new approach for calculating the sputtering of an atmosphere by impacting particles when there are molecular species at the exobase. We couple a test particle Monte Carlo approach with a molecular dynamic model to describe the collisions between hot particles and cold molecules in the Martian atmosphere. It is shown that both the heating efficiency and sputtering by pickup ions are reduced from that in an atomic thermosphere. The yields are given for three different ratios of atoms to molecules at the exobase and are used to obtain a better estimate of the total loss of atmosphere due to the pickup ion sputtering. Using the pickup ion fluxes of Zhang et al. <1993>, ~120 mbar of O and ~60 mbar of CO2 are lost. The loss of O if associated with H2O would be equivalent to ~4 m averaged over the Mars surface.