A topological insulator Bi2Se3 which shows superconductivity due to Cu doping has been studied using high resolution transmission electron microscopy. For the first time, this study reveals the presence of intercalated structure at nanoscale within the bulk material which is supposed to be the prime reason for superconductivity in doped topological insulator. A careful study exhibits the presence of two intercalation sites in this material when projected along the [?1?1 0] direction. Stoichiometry of the intercalated unit cell was also calculated from the projected mean inner potential.