Individual carbon nanotubes are filled with fullerene molecules directly on the substrate. Two different oxidation techniques for opening the tubes prior to the filling, annealing in air, and acid treatment, are compared. High-resolution transmission electron microscopy images indicate that both methods induce defects on the sidewalls of the nanotubes. In the case of acid treatment, the inner walls can be damaged without affecting the outer walls, while the inner walls are opened along with the outer ones by heating in air. The effect of acid treatment on the tubes is much stronger than known from bulk samples. In contrast to previous studies, we find amorphous carbon inside the nanotubes after oxidation, and an additional high-temperature annealing step is needed to remove these plugs in order to open the tubes for filling.