Single wall carbon nanotubes (SWNTs) have been processed in different schemes to get clean material for use in various filling experiments. The SWNTs synthesized by different methods require different processing schemes, and this is presumably due to heterogeneous nature of the various contaminants present along with the carbon nanotubes. For the pulsed laser synthesized SWNTs, a combination of nitric acid, hydrogen peroxide and hydrochloric acid treatment gives best results and the purified SWNTs give best ever filling fraction for fullerene, C60 of ~90%. The processing improves the surface cleanliness of SWNTs, in turn giving greater access for the target molecules, and hence the higher filling fraction. For the carbon arc produced SWNTs, air oxidation followed by treatment with nitric acid has been found to work best and the processed SWNTs have been used for filling experiments with metal chlorides. Both these processing schemes still leave a small fraction of catalyst impurities in the final material, thus the material quality of filled material and hence its properties depend on the processed material used for the filling experiments.