A bilayer of bismuth is recognized as a prototype two-dimensional topological insulator. Here we present a simple and well reproducible top-down approach to prepare a flat and well ordered bismuth bilayer with a lateral size of several hundred nanometers on Bi₂Se₃(0001). Using scanning tunneling microscopy, surface x-ray diffraction, and Auger electron spectroscopy we show that exposure of Bi₂Se₃(0001) to atomic hydrogen completely removes selenium from the top quintuple layer. The band structure of the system, calculated from first principles for the experimentally derived atomic structure, is in excellent agreement with recent photoemission data. Our results open interesting perspectives for the study of topological insulators in general.