/<FN\Q$i++\E>(.+)\n/

##</code><code>##

/<FN(?{$i++})(.+)\n/

##</code><code>##

while (<FILE>) {
    chomp;  #if necessary
    if ($_ =~ m/<FN\d+>(.+)\n/) {
        push @fnote, $1;
    }
}
my $numfootnotes = scalar @fnote;