use strict;
my @file = qw(file1.txt file2.txt file3.txt);

# read all files into one big 3D matrix
my $data = [];
for my $i (0 .. $#file) {
  open DATA, '<', $file[$i] or die;
  while (<DATA>) {
    chomp;
    my @line = split /\s+/, $_;
    my $linenum = shift @line;
    $data->[$_][$linenum][$i] = shift @line for (0..$#line);
  }  
}

# output to files for each variable
for my $n (0 .. $#$data) {
  open FILE, '>', "var$n.txt" or die;
  select FILE;
  for my $linenum (0 .. $#{$data->[$n]}) {
    print join "\t", $linenum, @{$data->[$n][$linenum]}, "\n";
  }
  close FILE;
}

##</code><code>##

0 0 1 2 3 4 5
1 0 1 2 3 4 5
2 0 1 2 3 4 5

##</code><code>##

0	0	0	0	
1	0	0	0	
2	0	0	0

##</code><code>##

0	1	1	1	
1	1	1	1	
2	1	1	1

##</code><code>##

0	2	2	2	
1	2	2	2	
2	2	2	2

##</code><code>##

0	3	3	3	
1	3	3	3	
2	3	3	3

##</code><code>##

0	4	4	4	
1	4	4	4	
2	4	4	4

##</code><code>##

0	5	5	5	
1	5	5	5	
2	5	5	5