I am going to hazard a guess and assume that you are wanting to do structural fillets. You may also want them to be "finished" fillets or "aero" fillets, so an "all-in-one" fillet. That is harder to do with CF. Most chopped CF will make the epoxy a bit lumpy and harder to control, but will result in a strong fillet. On the other hand, milled fiber will work better as it is essentially a powder and is much easier to mix in to make a more homogenized fillet. Not as strong as a CF fillet, but stronger than epoxy by itself (which is pretty brittle).
Last night I was reading some information from Jim Jarvis (a great composite rocket craftsman) regarding fillets, who mixes milled fiber and a bit of fumed silica (Cab-o-sil) to create what is called a
non-Newtonian fluid, so that once you get the shape desired for your fillet it will maintain that shape until the epoxy sets.
Greg