Shubnikov-de-Haas oscillations were studied under high magnetic field in Bi$_2$Se$_3$ nanostructures grown by Chemical Vapor Transport, for different bulk carrier densities ranging from $3times10^{19}text{cm}^{-3}$ to $6times10^{17}text{cm}^{-3}$. The contribution of topological surface states to electrical transport can be identified and separated from bulk carriers and massive two-dimensional electron gas. Band bending is investigated, and a crossover from upward to downward band bending is found at low bulk density, as a result of a competition between bulk and interface doping. These results highlight the need to control electrical doping both in the bulk and at interfaces in order to study only topological surface states.