As another possible idea, you could just use a split.

#!/usr/bin/perl
use warnings;
use strict;

while (<DATA>)
{
  next if /^NAME/ or /^\s*$/; #update changed \s+ to \s*
  
  print ''.(split (' ',$_,2))[1];
}
=prints
HT00000000    I
HT00000000    S
HT00000000    I
HT00000000    M
HT00000000    I
HT00000000    I
H000000000    I
H000000000    O
H000000000    I
=cut

__DATA__
NAME                           PT #          AT        

DOE                            HT00000000    I
DOE                            HT00000000    S
DOE                            HT00000000    I
SMITH                          HT00000000    M
DOE                            HT00000000    I
DOE                            HT00000000    I
DOE                            H000000000    I
DOE                            H000000000    O
SMITH                          H000000000    I
[download]

update: See above reply to stevieb.

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