my @files = qw(File1.txt File2.txt);
my %tree;
my(@iterations, @names);  # order
foreach my $file (qw(File1.txt File2.txt)) {
    open my $fh, '<', $file or die "Cannot open file $file: $!";
    (my $name = $file) =~ s/\.\w+$//;  # remove extension
    push @refs, $ref;  # order
    my($iteration);
    while(<$fh>) {
        chomp;
        if(/^Iteration /) {
            $iteration = $_;
            push @iterations, $iteration unless $tree{$iteration};  # key order
        } elsif(my($i) = /^(\d+):/) {
            $tree{$iteration}[$i]{$name} = $_;
        }
    }
}