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In the present study we investigated the nanostructuring processes in locally suspended few-layer graphene (FLG) films by irradiation with high energy ions (Xe, 26–167 MeV). For such an energy range, the main channel of energy transfer to FLG is local, short-term excitation of the electronic subsystem. The irradiation doses used in this study are 1 × 1011–5 × 1012 ion/cm2. The structural transformations in the films were identified by Raman spectroscopy and transmission electron microscopy. Two types of nanostructures formed in the FLG films as a result of irradiation were revealed. At low irradiation doses the nanostructures were formed preferably at a certain distance from the ion track and had the form of 15–35 nm “bunches”. We assumed that the internal mechanical stress that arises due to the excited atoms ejection from the central track part creates conditions for the nanodiamond formation near the track periphery. Depending on the energy of the irradiating ions, the local restructuring of films at the periphery of the ion tracks can lead either to the formation of nanodiamonds (ND) or to the formation of AA’ (or ABC) stacking. The compressive strain value and pressure at the periphery of the ion track were estimated as ~0.15–0.22% and ~0.8–1.2 GPa, respectively. The main novel results are the first visualization of ion tracks in graphene in the form of diamond or diamond-like rings, the determination of the main condition for the diamond formation (the absence of a substrate in combination with high ion energy), and estimates of the local strain at the track periphery. Generally, we have developed a novel material and have found how to control the film properties by introducing regions similar to quantum dots with the diamond interface in FLG films.