Device structure and fabrication methods for a bipolar junction transistor. One or more trench isolation regions are formed in a substrate to define a device region having a first width. A protect layer is formed on a top surface of the one or more trench isolation regions and a top surface of the device region. An opening is formed in the protect layer. The opening is coincides with the top surface of the first device region and has a second width that is less than or equal to the first width of the first device region. A base layer is formed that has a first section on the device region inside the first opening and a second section on the protect layer.