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:

use File::Marker;

my $file = File::Marker->new( $filename );

# make the (zero-based) index 
my $i = 0;
while ( ! $file->eof ) {
    $file->set_marker($i++);
    <$file>;
}

# save and rewind
$file->save_markers( $index_filename );
$file->goto_marker('LAST'); # rewind
[download]

Re-use the index

use File::Marker;

my $file = File::Marker->new( $filename );

$file->load_markers( $index_filename );

$file->goto_marker( 22 ); # start of 23rd line
[download]

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.