The sterile insect technique (SIT), which is based on irradiation-induced sterility, and incompatible insect technique (IIT), which is based on Wolbachia-induced cytoplasmic incompatibility (a kind of male sterility), have been used as alternative methods to reduce mosquito vector populations. Both methods require the release of males to reduce fertile females and suppress the number of natural populations. Different techniques of sex separation to obtain only males have been investigated previously. Our work involves an application of mechanical larval-pupal glass separators to separate Wolbachia-infected Aedes aegypti males from females at the pupal stage, prior to irradiation, and for use in a pilot field release and to assess the quality of males and females before and after sex separation and sterilization. This study was the first to demonstrate the efficiency of mechanical glass separators in separating males for use in an Ae. aegypti suppression trial by a combined SIT/IIT approach. Our results indicated that male and female pupae of Wolbachia-infected Ae. aegypti mosquitoes were significantly different (p < 0.05) in weight, size, and emergence-time, which made it easier for sex separation by this mechanical method. During the pilot field release, the percentage of female contamination was detected to be quite low and significantly different between the first (0.10 ± 0.13) and the second (0.02 ± 0.02) twelve-week period. Both males and females were almost completely sterile after exposure to 70 Gy irradiation dose. We observed that both irradiated Wolbachia-infected males and females survived and lived longer than two weeks, but males could live longer than females (p < 0.05) when they were irradiated at the same irradiation dose. When comparing irradiated mosquitoes with non-irradiated ones, there was no significant difference in longevity and survival-rate between those males, but non-irradiated females lived longer than irradiated ones (p < 0.05). Mechanical sex separation by using a larval-pupal glass separator was practically applied to obtain only males for further sterilization and open field release in a pilot population suppression trial of Ae. aegypti in Thailand. Female contamination was detected to be quite low, and skilled personnel can reduce the risk for female release. The irradiated Wolbachia-infected females accidentally released were found to be completely sterile, with shorter life span than males.