Over the years all my rods have accumulated some "war wounds" from doing battle with brush and tree bark, or in banging around in my car. They appear to be only cosmetic blemishes. What I do, is to paint on a little drop of thinned clear lacquer -- ie. the fly head cement I have at my tying bench. That remedy blends the scratch mark with the finish of the rod blank. It is a quick, easy, low-cost solution which works well for blending/hiding cosmetic scratches.
If the scratches appear to be more than cosmetic you may have to go to an epoxy type rod finish product to fill and bond with the rod finish.
Remember, even if you use your rod as intended you will get some "owies" in due course. So, appreciate them for what they are, badges of honour honestly earned. The only way to keep your rod in mint condition is to keep it in its case. And that's no way to treat a good Spey rod. . . Rods need to breathe!
Cheers!