This article presents methods for detailed physical analysis of partial steps leading to the removal of residual metal catalyst nanoparticles (NPs) from single walled carbon nanotubes (SWCNTs) and options for detecting negligible amounts of metal in samples possessing diamagnetic response. Based on the previous knowledge of the composition, structure and magnetic properties of NPs included in the commercial HiPco_raw and HiPco_SP SWCNTs, the properties of remaining NPs after the multi-step purification (oxidation followed by mild acid treatment) and annealing both under static and dynamic vacuum have been investigated. Thermogravimetry, X-ray diffraction, static and dynamic magnetic property measurements and the Extended X-ray Absorption Fine Structure (EXAFS) experiments have been performed. The data provide information about the nature of the residual NPs in purified SWCNTs, which is crucial for further understanding of the purification processes and their improvement. It has been demonstrated that even if all macroscopic methods indicate a high purity of the treated sample, a non-negligible amount of the metal may still be present and the metal content has to be examined using local and element sensitive probes such as EXAFS.