Remove it and have it ceramic coated if it bugged you that much :-)

 

OK, lots of folks here that don't know the Honda factory S2000 header is made from stainless steel. Stainless can rust and is a misnomer. If you want to make it pretty polish it up. I did mine a few years back and it came out very nice.

https://www.s2ki.com/s2000/gallery/i...3-dsc00196jpg/

 

You can clean it up with some penetrating oil. It will season it a little. The rust will be more of a dark uniform color, instead of that bright flash rust.