Owing to superior physical properties such as high electron saturation velocity and high electric breakdown field, GaN-based high electron mobility transistors (HEMTs) are capable of delivering superior performance in microwave amplifiers, high power switches, and high temperature integrated circuits (ICs). Compared to the conventional D-mode HEMTs with negative threshold voltages, enhancement-mode (E-mode) or normally-off HEMTs are desirable in these applications, for reduced circuit design complexity and fail-safe operation. Fluorine plasma treatment has been used to fabricate E-mode HEMTs, and is a robust process for the channel threshold voltage modulation. However, there is no standard equipment for this process and various groups have reported a wide range of process parameters . In this work, we demonstrate the self-aligned enhancement-mode AlGaN/GaN HEMTs fabricated with a standard fluorine ion implantation. Ion implantation is widely used in semiconductor industry with well-controlled dose and precise implantation profile.