We evaluated the trade off between damage generation and particle removal of single wafer aerosol spray and megasonic cleaning tools. This was done by the calculation of the local particle removal rates of 30 nm silica and the local damage fluxes of ~ 20 nm wide amorphous-Si lines.Cleaning and damage nonuniformities observed for aerosol cleaning were due to different exposure times to the spray nozzle. The non-uniformities for megasonic cleaning were due to different exposure times to the rod as well as to non-equivalent acoustic energy transmission across the wafer. Furthermore the extent of cleaning for equivalent damage generation was shown to be comparable for both techniques, but far from specification for the experimental conditions used here.