If you have a large number of flies, then some sort of breeding ground exists nearby. Open trash cans, pet feces, an improperly managed compost pile, and empty yet dirty bottles can all provide fly breeding grounds. Keep lids on trash cans and attend to your compost pile to be sure sufficient heat exists to kill fly larvae. The addition of a small amount (about 1% of the feed weight) of diatomaceous earth to your pet's food will control internal parasites and prevent flies from breeding on your pet's feces.
For the occasional fly, keep a spray bottle of rubbing alcohol present. Douse any flies that are a nuisance. A common fly swatter will also work. Use a non-chemical fly trap if your problem has escalated or if the flies are of a biting nature.