Burn a scented candle if you don't have incense.. "Burn a little incense. The very small respiratory systems of fruit flies are delicate, and require a constant supply of clean air. This means that inhaled irritants, such as smoke, can kill them relatively quickly. Although you can’t set a fire in your house, you can burn incense. The smoke and perfume put off by these sticks will drug your flies into a slow death."