That isn't a Perl problem. Your web server isn't configured to do what you want it to do. It hasn't been told to treat the file as a CGI script.

If you want to treat all .cgi files in a directory and subdirectories as CGI scripts:

<Directory /some/dir/htdocs/>
   Options +ExecCGI
   AddHandler cgi-script .cgi
</Directory>
[download]

If you want to treat all files in a directory and subdirectories as CGI scripts:

<Directory /some/dir/cgi-bin/>
   Options +ExecCGI
   SetHandler cgi-script
</Directory>
[download]

There's also ScriptAlias.