I've found that running the code through perltidy (using the same format) is a good idea, it will transform code to be uniformly formatted. That way, whitespace differences etc are eliminated as a source of difference between two pieces of code. Obviously, you should run the perltidy script before any other systems that searches your codebase for duplicate code or near-duplicate code. Using perltidy will improve the false-positive rate of the other systems.
(You can even enforce a uniform coding format by using perltidy with the available hooks in source control products, but that's a different subject)