I have a second mortgage on my home... the original amount was like 13,500.00. No payments have been made for a long time on it. There is a lien against my home for the original amount. I am refinancing and when I called the co. for a pay off on the second mortgage they gave me some ungodly amount like 27,000.00 for interest and late charges. Legally do I have to pay the bigger amount or just what the lien against the home is for?

You have to pay what you owe. If your contract included interest accruals and late charges then that's what you owe. You might try negotiating with them, but with a lien, they have the leverage.