Strict sanitation measures in your home are suggested to control bottle flies and to prevent an infestation. Sewer pipes should be inspected for breaks. Animal feces should be removed. Garbage storage areas should be carefully cleaned and garbage cans should equipped with tight lids. Rotting produce and other food products should be promptly removed from the house. A dead animal, perhaps hidden inside a wall or as a result of a mousetrap, can lead to problems with bottle flies.
Tightly closed windows and doors and window screens that are in good condition can help prevent bottle flies from entering a house. Cracks or openings around doors and windows should be caulked. Fly strips and aerosol insecticides can be of some use in controlling the number of flies you see, but a pest control professional should be contacted as soon as possible in case of a serious infestation.