Use photoshop to create a blue (or green) shape that is the approx
the size that you need for the blur. Make sure to make the background
transparent. You can also blur the edges in photoshop to clean it up.
Now import that shape into fcp and place it on top of the clip that
you need blurred. Use key frames to move the shape around and keep
the area in question covered. When you are satisfied that everything
is covered up export your timeline as a self contained file.
Import that file and place it on top of the original clip.
Make sure they are still in sync (you can crop it in half to check).
Apply the blur filter to the clip on bottom.
Now, key out the blue shape to let the blur show through.
If you do it right it should look fine.
I had to do something like this yesterday and was pretty
impressed with the results.