If you are using an SEO plugin like squirrly SEO or Yaost you can exclude them from the sitemap very easily. I am using Squirrly SEO and under the tab Squirrly > SEO Settings > Automation, I chose to exclude them from my sitemap. These are essentially theme template files. I have also added a nofollow tag to the templates.
Im guessing just about any SEO plugin has this feature.