.NET Web Project from local IIS, exclude virtual directory from publish

.NET Web Project from local IIS, exclude virtual directory from publish

I had a file system only web project solution. I needed to convert it to
use IIS. So, I mapped a site in IIS to the path where the solution
existed. In visual Studio I opened the solution from local IIS Site, bam,
everything is great.
Except, now, when I publish the solution (to deploy to another webserver)
it makes full copies of the virtual directories.
I do not need these as physical copies, obviously the point of a virtual
directory is to point to an already existing path somewhere.