I'm not sure I know what you mean, but I think you want to run the perl program in the active buffer.

First up, get mode-compile from http://www.tls.cena.fr/~boubaker/Emacs/ and a recent cperl-mode from http://www.ilyaz.org/software/emacs/.

The emacs wiki has lots of stuff about cperl-mode and mode-compile.

I have mode-compile bound to F12 with (global-set-key [f12] 'mode-compile) so I just press F12 to run the Perl program I'm currently editing.