Smaller indoor flies, like the fruit fly or the drain fly are capable of breeding and living entirely indoors.  Like most flying insects, these flies are also most commonly found during the warmer months. Sanitation is again the key to controlling their presence in and around homes and businesses.  Fruit flies are found in trash cans, especially with spilled liquids, bagged vegetables, overripe or rotten fruits, open cans/bottles of liquids, floor drains etc. While fruit flies do not bite in sterile environments, they can cause health risks through contamination. Drain flies are also small indoor pests. Unlike the fruit fly, drain flies feed on bacteria and fungi that can be found in drains, air conditioners, garbage cans, refrigeration condensation pans etc. 

Sanitation is by and large the most efficient and effective way to control most fly species.