I'm looking for a flat bottom paper filter that fits a basket about 3" on the bottom and 2.5" high. #2 cone filters work, but are really not ideal. The basket belongs to a Cuisinart coffee maker.
There are "basket-shaped" filters, which I think is what you're looking for. In my area, they're just as common as "Melitta-style" cone-shaped filters; you should be able to find them at most markets / grocery-stores. They come in various sizes; you're probably looking for one of the smaller ("junior size") variety.
From this previous answer, here's a picture of what you're looking for, I think: a basket-style filter:
You can also find them online -- one example of the "junior size" basket filter, which is what I think you want based on what you said about the size of the machine/filters. There are 3 main sizes (and probably more): "junior size" (for ~2-6 cup machines -- as linked above), the most common normal/medium size (for 8-12 cup machines), and the large/extra-large size (for large/commercial 20+ cup machines).
They tend to be inexpensive and come in large packs... I hope you drink a lot of coffee ;-)