Derek - I'm not seeing any pics - try re-posting.
1st: Are you sure the worms are gone?
2nd: Are these long marks along the surface or narrow holes into the wood? If not narrow holes, about how wide?
3rd: Are there a lot of holes concentrated in one area, so that the integrity of the wood is compromised?
If you have relatively narrow holes a good solution is wax sticks. They come in dozens of different colors and cost about $2. You can get them from repair sites (see below) or you can buy regular crayons in an art supply store. After wood is stained and dry, and before finish is applied, you rub these over the holes. They fill the holes in a matching color, and you scrape off excess. You can apply oil base finishes right over them. If using water base finish, then apply a diluted coat of Sealcoat, let dry, light sand, and apply the WB finish.
Here are some repair sites:http://www.hoodfinishing.com/Products_I ... oducts.pdfhttps://woodfinishersdepot.com/touch-up ... ticks.htmlhttp://homesteadfinishingproducts.com/t ... ents-misc/