Hi geoff, there is nothing set up inside of the Fillet command itself to do that particular thing but you can probably use alternate techniques to get what you want.

Probably try sweeping a circle along your edge to form a tube object, then use the tube as the cutting object in a boolean difference, similar to what is described here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=817.8

If that does not do what you need maybe you could post the 3DM model file of the thing you're working on so it will be easier for me to figure out what you are trying to do.

- Michael