Master of all things exhaust says: if it's a titanium can, take a Scotch-Brite pad and scuff the entire sleeve of the muffler - it'll give you a soft, consistent finish that looks very nice (Yoshi ti cans actually come with a pad for this purpose). If it's carbon, you might be able to cover the scratch with a large black Sharpie. If it's polished aluminum and the scratches are at all deep, you're likely going to have to live with it.
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