Did you try with perltidy? I've it integrated to emacs with the following code in the .emacs 
(global-set-key "\C-xt" 'perltidy-region)
(defun perltidy-region ()
  "Run perltidy on the current region or the whole buffer."
  (interactive)
  (save-excursion
    (let ((beg (if mark-active (point) (point-min)))
          (end (if mark-active (mark) (point-max)))) 
      (shell-command-on-region beg end "perltidy -q" nil t))))

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Originally from Specific Indentation request for perl in Emacs and then I modified it a little bit, so before checking in my code I run it thru perl tidy by pressing Ctrl+xt

In reply to Re: CPerl-Mode Indentation by bluescreen
in thread CPerl-Mode Indentation by azbok

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