G'day edge99off,

Welcome to the Monastery.

Unfortunately, a prosaic description, such as you have here, doesn't provide us with sufficient information to offer much help.

What we really need to see is: a minimal piece of code that's shows what you're currently doing; a small, yet representative, sample of your data; what your current results are and how they differ from what you want; and, possibly any messages (e.g. warnings or errors) that you're currently receiving. You'll find details of this in "How do I post a question effectively?".

On the basis of what you've posted, here's some potential help.

Use the Text::CSV module to parse your CSV files.

"REGEX or pattern matching" doesn't make a lot of sense (at least, not in the context you've used here). You use a regex for pattern matching; not as an alternative. Maybe, when you post some code, your meaning will become clearer. Perhaps take a look at "perlintro: Regular expressions" and follow the links therein for more information.

Reading a file will not damage it. Parsing its data will not damage the file. The way you open your files could be an issue. Again, this is another example where seeing your code will clear this up for us.