Device structures and fabrication methods for a bipolar junction transistor. A first semiconductor layer is formed on a substrate containing a first terminal. An etch stop layer is formed on the first semiconductor layer, and a second semiconductor layer is formed on the etch stop layer. The second semiconductor layer is etched to define a second terminal at a location of an etch mask on the second semiconductor layer. A first material comprising the etch stop layer and a second material comprising the second semiconductor layer are selected such that the second material of the second semiconductor layer etches at a greater etch rate than the first material of the etch stop layer. The first semiconductor layer may be a base layer that is used to form an intrinsic base and an extrinsic base of the bipolar junction transistor.