We present a direct atom-by-atom chemical identification of the nanostructures and defects of topological insulators (TIs) with a state-of-the-art atomic mapping technology. Combining this technique and density function theory calculations, we identify and explain the layer chemistry evolution of Bi(2)Te(3–x)Se(x) ternary TIs. We also reveal a long neglected but crucially important extended defect found to be universally present in Bi(2)Te(3) films, the seven-layer Bi(3)Te(4) nanolamella acceptors. Intriguingly, this defect is found to locally pull down the conduction band, leading to local n-type conductivity, despite being an acceptor which pins the Fermi energy near the valence band maximum. This nanolamella may explain inconsistencies in measured conduction type as well as open up a new route to manipulate bulk carrier concentration. Our work may pave the way to more thoroughly understand and tailor the nature of the bulk, as well as secure controllable bulk states for future applications in quantum computing and dissipationless devices.