The focus of this work is to fabricate AlGaN/GaN high electron mobility transistors (HEMTs) and provide feedback to the MBE lab. Cl2-based GaN reactive ion etching, as a critical step of HEMT process flow, is investigated to obtain consistent etch rates with smooth etched surfaces. The adverse micromasking effect is largely mitigated. The atomic force microscopic study show the roughness of etched GaN surfaces is comparable with that of the as-grown surface. A more predictable etch rate is also obtained, ~ 110 nm/min at a plasma power of 150 W with reduced etch damage. HEMTs are fabricated using AlGaN/GaN samples grown both by molecular beam epitaxy (MBE) system at Notre Dame and by metal organic chemical vapor deposition (MOCVD) at UCSB for comparison. The current MBE HEMTs exhibit smaller currents and higher buffer leakage due to the lower charge concentrations, low carrier mobilities and poor regrowth interfaces. Flourine-treatment to reduce gate leakage is also attempted. The preliminary results are summarized.