I would treat this just as I would if purchasing any used car. The
seller needs to ensure that the lien is removed. Otherwise, no deal.
Option 1: The seller pays off the loan, and gets the lien removed. The seller then gets the title re-issued to himself (showing no lien), and hands you the clear title when you buy the car.
Option 2: You meet with the seller at the lien-holding bank. You and the seller meet with the loan officer, and you give your check directly to the bank. The loan officer of the bank then issues the 'release of lien' directly to you, which you can then take with you.
Any other type of arrangement is a show-stopper, and you should not agree to it. It is the seller's responsibility to provide a clear title with no liens...period. Anything else involves too much risk of fraud, and too much possiblity of hassle when you get the car titled.
-Tom