Fabrication of sub-micron high electron mobility transistors (HEMTs) involves dry etch removal of GaAs from an underlying AlGaAs or InGaAs stop layer. The etch selectivity is achieved by formation of AlF3 on AlGaAs, or InCl3 and InF3 on InGaAs, which must be removed before processing can proceed. Wet chemical cleaning has difficulty in such a situation because of surface tension effects. We have investigated use of Electron Cyclotron Resonance (ECR) H2 or Ar discharges, or hexafluoroacetylacetone (HFAC) vapor, for in-situ dry etch cleaning of HEMTs exposed to low bias BCl3/SF6 discharges. The HFAC vapor can remove most of the remnant fluorine, but is effective only when the sample is heated above ∼250°C. This relatively high temperature is not compatible with in-situ cleaning of the etched device. Low-bias(−75V) sputter cleaning with an Ar discharge removes all remnant Cl and ∼40% of the F, but dc biases above -125V are required for complete cleaning, and this ion bombardment can lead to damage in the HEMT. ECR H2 discharge exposure is effective in removing all Cl- and F-related residues in a short period (∼5 mins) with low dc biases (−25 V) on the sample.