For carbon nanotubes filled with fullerenes (“peapods”), it is a key issue to find an analytical method that distinguishes the molecules inside the nanotube from those adsorbed on its surface. High-resolution transmission electron microscopy (HRTEM) detects both encapsulated and adsorbed molecules which are large enough (e.g., fullerenes), but being a local-probe method, it cannot be applied to large amounts of sample. In Raman spectroscopy, the empirical rules for line shifts and splitting are nanotube-type dependent and often ambiguous. We prepared C60 peapods by nano-extraction using supercritical CO2 as a solvent, and subsequently removed the adsorbed fullerene molecules by washing the samples. We analyzed the samples by the combination of HRTEM, Raman, and midinfrared attenuated total reflectance (MIR-ATR) spectroscopy. Although the TEM images proved that the nanotubes were filled with fullerenes, we did not observe any shift in the fullerene's Ag(2) Raman mode compared to C60 crystals. ATR spectra, on the other hand, were found to detect only the adsorbed molecules. Therefore, the combination of the two methods provide good basis for determining the success of nanotube filling by spectroscopy alone.