Single walled carbon nanotubes (SWCNTs) can be modified to produce a new concept of hybrid materials by introducing atoms or molecules inside their cylindrical empty space. Such an endohedral doping of the SWCNTs is expected to decisively alter their electronic transport and mechanical properties, In this study, we purified SWCNTs by three-step purification processes and formed the peapod structure by introducing $C_{60}$ fullerenes inside the SWCNTs. $C_{60}$ molecules were observed to be regularly arranged by transmission electron microscopy. In Raman spectra, the radial breathing mode (RBM) rather than the other modes was significantly affected by the endohedral injection of $C_{60}$. The RBM intensity was more greatly reduced in the large-diameter SWCNTs than the small-diameter ones, Raman spectroscopy is expected to be a key technique for analyzing $C_{60}$-encapsulated SWCNTs.