We present STM/STS, ARPES and magnetotransport studies of the surface topography and electronic structure of pristine Bi2Se3 in comparison to Bi1.96Mg0.04Se3 and Bi1.98Fe0.02Se3. The topography images reveal a large number of complex, triangle-shaped defects at the surface. The local electronic structure of both the defected and non-defected regions is examined by STS. The defect-related states shift together with the Dirac point observed in the undefected area, suggesting that the local electronic structure at the defects is influenced by doping in the same way as the electronic structure of the undefected surface. Additional information about the electronic structure of the samples is provided by ARPES, which reveals the dependence of the bulk and surface electronic bands on doping, including such parameters as the Fermi wave vector. The subtle changes of the surface electronic structure by doping are verified with magneto-transport measurements at low temperatures (200 mK) allowing the detection of Shubnikov-de Haas (SdH) quantum oscillations.