Thanks so much for the great answers.  Pulling the nails through, in most cases here, is not an option.  Removing the treads where they are embedded would be more of the same and more trouble.

For clarification, the finish nails had been shot into the banister itself in some of the joints and at the underside of the banister where the stiles fit into the banister and on the tread where the stiles meet the treads.  The application of nails in the joints of the banister was an attempt by the builder to improve his alignment of the banister… now you get an idea why I am removing the banister and newel posts.  I’m just going to start over.

Thanks again for the help everyone!

Jerry