We have fresh fruits and vegetables in the warehouse at work, and occasionally we get some up in the office.
We take a slice of lemon (or limes, or tomatoes or whatever, sometimes a combination) in a glass or mug. Put a piece of Saran wrap over that and put some tiny little slits in the wrap. The food entices the flies in, but they can't get out again. When there is some in the mug, put it in the freezer. They are so small they freeze almost right away. We cover it with a saucer or something to ensure they are trapped before moving the mug. Periodically we pour vinegar down the drain to flush them out of there. And yes, it can take several days to get rid of them all.
We don't have a garage disposal so can't try the ice trick.