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;
}