A stick of green shellac (lapidary supplies) and a small stick will hold them fine. Melt a dab of the shellac onto the end of the stick, and while it is still a bit molten, stick the flint into the shellac, flat side down. Now you have means of holding it, and you can diamond file it, use your grinder, however you want to flatten the top.
Now, two ways to get it off the stick and shellac: You can stick it in the freezer for half an hour or so, then just tap on the flint. Or you can heat the shellac again and take the flint off.. If you use the second method, have the next flint ready to stick into the hot shellac.
From the lapidary supply store, you can also get diamond wheels of various grits and use them to shape your flints.