seek, or close and re-open the file. ...or make your filehandle lexically scoped to a block just outside your while loop (which will handle closing your file for you). In other words:

{
    open my $fh, '<', $filename or die $!
    while ( <$fh> ) {
        # do your stuff.
    }
    # Note, your $fh is about to pass out of scope, which
    # will close the filehandle in cleanup.
}
{
    $open my $fh, '<', $filename or die $!
    while ( <$fh> ) {
        # do your other stuff.
    }
}
# Now the second filehandle fell out of scope and closed too.
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