|laziness, impatience, and hubris|
This would probably be a lot more useful if it were implemented as a subclass of Tie::File.
Actually, this seems like a job for inside-out objects. I just uploaded to CPAN a new, quick-and-dirty version of File::Marker (0.11) that adds the ability to save/load markers from an external file. It works similarly to what you've described, though you have to do the line-numbering work yourself. On the flip side, it handles the seeking for you and works like an IO::File object (which it subclasses).
Creating the index:
Re-use the index
You could probably extend it to focus on line-numbers instead of marking any type of position in a file or add the various special features people have mentioned. Alternatively -- perhaps even better -- would be to reimplement it using Class::InsideOut, since File::Marker is only really intended to be a teaching module. If I get around to figuring out how to sanely and safely serialize IO::File based inside-out objects with Storable, this could be even easier.
Code written by xdg and posted on PerlMonks is public domain. It is provided as is with no warranties, express or implied, of any kind. Posted code may not have been tested. Use of posted code is at your own risk.