So what have you tried?

Welcome to the Monastery (and be not offended; many new monks have had a first post get that for an initial answer).

But we'll likely be more helpful if you:

1. Post the script you've tried, along with an explanation of how (error messages, warnings, unexpected or no output) it fails to do what you want.
2. Be a bit more specific about your data: are the source files text (free text), CSV, out of a DB or what.
3. Read How do I post a question effectively? and Markup in the Monastery

If you haven't written any code yet, you might want to think about these semi-random observations:

• Do you have enough RAM to read "~ 100,000 rows" (x 2 ???) into memory at once? That may determine the manner in which you proceed.
• If you're just starting Perl and have no programming experience, you may need to tackle simpler tasks before tackling this one. In that case, you're in the right place: see Tutorials, use Super Search and consider a book such as Learning Perl.