We investigated the properties of a citric acid-based GaAs/InGaP selective wet etchant. We found that the citric acid-based etchant has a much higher selectivity and exhibits less undercutting than those of a conventional sulfuric acid-based etchant that we had used. Then, we applied the citric acid-based wet etchant to the fabrication of via holes with high thermal diffusibility underneath heterojunction bipolar transistors. The citric acid-based etchant exhibited GaAs/InGaP selectivity of about 9800 at pH 9.0 and enabled reliable etch stopping without pinholes. The citric acid-based etchant also suppressed undercutting and enabled the integration of the via holes. We used the optimized citric acid-based wet etching for finishing the via hole etching after rough high-speed wet etching with the conventional sulfuric acid-based etchant. The two-step wet etching process resulted in a successful fabrication of the sub-transistor via hole structure with collector-up heterojunction bipolar transistors.