I was trying to change the fuel filter on my 98 civic and stripped the bottom bolt. I got the top one off ok but the bottom one wouldnt come off for any thing. I went and got a flare wrench, but it was too late and the bolt is stripped. How can I get this off and can I just replace the bolt or will i need a new fuel line???

I would get a new filter at the parts store and purchase a 12 inch piece of brake line tubing that fits. Then find a splice connector that fits the fuel line.
You can use a flaring tool two flare nuts and a connector. You also need a tubing cutter. I've used a copper crimp connector for this pressure fuel line.
Don't cut the piece of brake line until everything is measured.
Dorman also probably makes a repair kit if you check.
http://www.dormanproducts.com/
Is this the correct end Honda uses a Bango bolt on the other end. The dealer should handle these.
http://www.ebay.com/ Search bango bolt socket.