sub process_file {
    my ($fh) = @_;

    while ( my $line = <$fh> ) {
        print $line;

        if ( $line =~ /section start marker/ ) {
            $line = handle_section($fh);
            redo if defined $line;
        }
    }
}
...
sub handle_section {
    ...
    return $line;
}