Make sure any food you put in the bin is covered with several inches of shredded paper. This keeps the fruit flies at bay.
With the ones you already have, set a little jar with a bit of cider vinegar and a drop of dishwashing liquid in, near the bins. You can even set it on top of the bedding inside the bin to catch the flies. I've only had a few fruit flies, but it works.
You can also vacuum them.

It takes months for a bin to be up and running to its potential.
3 dozen worms is very few. Do you have just 36 worms in a large rubbermaid bin?? I would use a very small container with that number. You have to be very careful you don't overfeed.
I currently have 50 worms in a plastic salad container mini-bin. I enjoy doing a mini-bin as well as my full size ones.

You can always just drape a piece of mosquito netting over the worm bin.

Here is a link that might be useful: Vermiculture Pests

Hi. I had a horrible fruit fly problem until I started freezing the food for 3 days before putting it in the bin. This kills the eggs that might be in the food, under the skins. That's where fruit flies lay their eggs. I also took my bin outside to open it and shooed the flies as best I could. I used a screen like african suggested, but I just used a piece of window screen. To get rid of the ones in the house, I sprayed Raid around the kitchen window. They are trying to get out where they see light. Hope this helps. No more fruit flies at my house.

Kath

Check this out:

http://forums.gardenweb.com/forums/load/verm/msg1219182832031.html