Fabrication methods for a bipolar junction transistor. A semiconductor material layer is formed on a substrate and a mask layer is formed on the semiconductor material layer. The mask layer is patterned to form a plurality of openings to the semiconductor material layer. After the mask layer is formed and patterned, the semiconductor material layer is etched at respective locations of the openings to define a first trench, a second trench separated from the first trench by a first section of the semiconductor material layer defining a terminal of the bipolar junction transistor, and a third trench separated from the first trench by a second section of the semiconductor material layer defining an isolation pedestal. A trench isolation region is formed at a location in the substrate that is determined at least in part using the isolation pedestal as a positional reference.