My first stab, thought up real fast, most likely not the best solution:

use strict;
use warnings;

my (@one, @two, @three);

while (<DATA>) {
  chomp;
  /([^ ]+) ([^ ]+) ([^ ]+)/;
  push @one, $1;
  push @two, $2;
  push @three, $3;
}

print join("\n", join(' ', @one), join(' ', @two), join(' ', @three)),
+ "\n";

__DATA__
1 cow MM
2 cat DD
3 fly SS
[download]