Many small flies(<1/4"th) are found in food prep areas and may carry disease causing organisms.
The five spiecies listed below are the most common of the small fly.

SMALL FLIES
Fruit Fly	Phorid Fly	Moth Fly (Drain Fly)
Sphaerocerid Flies	Fungus Gnats	Cheese Skipper

Breeding Sites:
These small flies may be found breeding in moist organic matter. This includes such places as soil contaminated with sewage or drains, decaying fruit or vegetables, and garbage.
Sphaerocerid flies are also found in manure; cheese skippers bred in meat, cheese and animal cadavers; and fungus gnats can feed on fungus growning in wet soil.

Where is Inspect -Tips:

• Moist organic matter
• Decaying plant/vegetable/fruit matter
• Dumpsters, compactors, trash cans
• Where equipment legs meet the floor
• Discarded fruit cans or soda cans and recycle bins
• Drains
• Elevator pits
• Under refrigerators in condensation pan
• Terrariums, soil in potted plants-particulary for the small fly called a fungus gnat Please read more on fungus gnats from this link in order to obtain better control.
• Mop buckets, mops
• Cadavers
• Grease or food trapped in cracks of equipment
• Leaks in or around cabinets that cause wood to stay moist.
• Wet insulation in walls and ceilings.

• Removing all breeding sites in the best method for eliminating a small fly infestation.

Unfortunately, bleach and hot water will not eliminate breeding sites in drains for the drain fly.
Drains need to be treated with a industrial strength drain cleaner such as :
A bacterial digester like   DF 5000 may be used to break up the organic debris.

Dry soil out, if flies are found in moist soil.
Place a 2" layer of sand over the dried soil will help prevent future breeding areas in the soil.

Remove sewage infested soil and replace with new soil if you have a Phorid Fly problem.

Clean and caulk cracks between floor and equipment.
Remember to dry out moist areas, because larvae need a moist area to survive.

Store meats and cheese between 30-36 degrees F.
Cheese Skippers can't infest properly stored meat and cheese.

After removal of breeding sites, a non residual pryethrin spray space spray KONK II can be used as a quick kill, reducing populations of flying insects.
Fogging material(pyrethrins) and professional fogger equipment:
Fogging Equipment and Fogging Material