This is not really a perl question, so I can't offer a perl answer. If you are really concerned about the security of these files, you will need to do quite a bit of reading. You have several things to consider: physical security, encryption, transmission, intrusion detection, and on and on. Far more than I can go into here. Then all this information is completely platform dependant. I would recommend the ORA books on security Prac Unix and Internet Security Securing Windows NT/2000 Servers for the Internet and Hacking Exposed 2nd Ed by Osborne.

As an admin directly responsible for security of NT, 2000 and Linux boxen, I would highly recommend leaning towards a *nix solution. I patch M$ products weekly without a break.

grep

grep> cd pub grep> more beer [download]