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You don't necessarily have to slide mount the specimen or even clear the genitalia; with a good microscope most specimens can be identified in alcohol. If you just need to see the genitalia, I suggest lactic acid is much safer than KOH or NaOH, with little chance of "overclearing" the structures. If you are going to slide mount the whole fly, then KOH, dehydration in clove oil, and mounting in Canada Balsam is what I'd recommend. Another option is to put the whole fly in lactic acid, identify it, then store it in glycerine in a microvial with the stopper pinned (a lazy, but convenient method).

Brian