Rubbing alcohol can kill fruit flies on contact. Fill a fine-misting spray bottle with rubbing alcohol and spray the fruit flies. The alcohol will kill them, and dead fruit flies can be cleaned up easily with a wet rag. However, it is important to avoid spraying the alcohol on fruit, as it may cause them to spoil, which will lead to more fruit flies. Other methods to get rid of fruit flies include trapping them with vinegar or beer, using a paper cone, and disposing of overripe or rotting fruit and vegetables.