I assume that you're worried that "pod comments" will appear in the output from any POD processing that you do on the file. The way round that is to use the =begin and =end directives. Any section that is marked as =begin comment will only be picked up by a POD processor that is specifically looking for content marked as a comment. No such processors (currently) exist, so your comments wouldn't suddenly start appearing in your documentation.

See perlpod for details.