Hi,
..I thought it would be easy to just load it into a hash and then be able to reprint it to a different file but it is not working since I can't figure out how to start back up at the top of a new column...

You could do this:

use warnings;
use strict;
use Data::Dumper;

my $title =<DATA>;
my %hash;

while(<DATA>){
 chomp;
 my $val = substr $_,0,1;
   push @{$hash{$val}},$_;
}

print Dumper \%hash;

__DATA__
a b c
0 0 d
0 1 d
0 1 d
0 2 d
0 2 d
1 0 d
1 0 d
1 1 d
1 1 d
1 2 d
1 2 d
[download]

which produces this..

$VAR1 = {
          '1' => [
                   '1 0 d
',
                   '1 0 d
',
                   '1 1 d
',
                   '1 1 d
',
                   '1 2 d
',
                   '1 2 d '
                 ],
          '0' => [
                   '0 0 d
',
                   '0 1 d
',
                   '0 1 d
',
                   '0 2 d
',
                   '0 2 d
'
                 ]
        };
[download]

UPDATE...
You now have the hash you wanted, and since you have the title, in variable "$title", you can use it anytime you want.
Though the printing out you desire is left for OP... :)
Hope this helps.