Nothing's *automatic* per se. Perltidy is a filter that you run on source. As TheDamian has it setup, it will print to STDOUT, so you can do something like this:

perltidy sloppy_format.pl > cleaned_up.pl

.perltidyrc will be automatically called for configuration details. Once you get that figured out, you can even hightlight one block in vim and do "! perltidy" to cleanup just a block within a file.

Good luck and perservere. Tidy code is a worthwhile endeavor, whether you create it that way or beat it into submission with a tool.