Atomic force microscopy (AFM) has become a versatile and powerful method for imaging both insulating and conducting objects down to the atomic scale. By extending the high spatial resolution and sensitivity of AFM to the force spectroscopy dimension, oscillations of individual molecules can be studied with atomic resolution. Using three-dimensional mapping of the force and damping fields we address individual Dy@C(82) metallofullerene molecules confined inside single-walled carbon nanotubes (so-called metallofullerene peapods) and reveal their oscillatory behaviour via attractive interactions with the AFM probe tip. The damping energy DeltaE signals, generated in very close proximity of the tip and nanotube peapod, show a close relationship with hysteresis in the short-range forces, thereby indicating that a soft vibrational (phonon) mode is site-specifically (i.e., atom-by-atom) induced by the AFM tip.