As Limbic said, we need more information to give better answers. But, if you are working with a delimited file, i would definately second the recommendation for DBD::CSV. It's saved my bacon more than a few times.

Then, of course, theres the by-hand option of reading in the contents of the file, using regexes and conditionals, and writing it all back out. But thats really just if you have a very unique situation (or if you like rolling your own a bit too much).