I cut down my fmf can drom the bottom (inlet side) and had the same problem with the starp leaving marks on it, and the marks being in a different place when the can was cut. idk how to clean up ti, or whatever material your can is made of, but i painted my can flat black, so that helped hide them.
and as far as cutting it, i agree the dremel would be a pain. i used a chop saw with a metal blade on it, the cut was a little rough but a lot cleaner and straighter than i could have gotten with a dremel or cut off wheel. then just cleaned it up with a file.
oh yeah TI makes a lot of cool white sparks to. haha