If only the second column can contain spaces, then by anchoring the regex at both ends and using a non-greedy match for column two you should be able to handle all the possibilities. This seems to. (I've added a couple of possible variations). 

#! perl -slw
use strict;

my @bits;
my $count = 0;

while( <DATA> ) {
    ++$count and print join'|', @bits 
        if @bits = 
        m[
            ^
            (.{3})
            \s
            (.*?)
            \s+
            (\S+)
            \s+
            (\S+)
            \s+
            (\S+)
            \s+
            (\S+)
            \s+
            (\S+)
            \s+
            (\S+)
            $
        ]x;
}

print $count;

__DATA__
BAZ 'N3''  N  0 ? ? ? 1
BAZ 'N4''  N  0 ? ? ? 1
BAZ 'C8''  C  0 ? ? ? 1
BAZ C9     C  0 ? ? ? 1
BAZ ZN     ZN 0 ? ? ? 0
BAZ HN1    H  0 ? ? ? 1
BAZ 1HN2   H  0 ? ? ? 0
BAZ 2HN2   H  0 ? ? ? 0
001 F11  F 0 ? ? ? 1
001 C11  C 0 ? ? ? 1
001 O 1 1  O 0 ? ? ? 1
001 N12  N 0 ? ? ? 1
001 C12  C 0 ? ? ? 1
001 C13  C 0 ? ? ? 1
001 C 14  C 0 ? ? ? 1
001 C15  C 0 ? ? ? 1
001 C16  C 0 ? ? ? 1
BCB CBA   C  0 ? ? ? 1
BCB C  GA   C  0 ? ? ? 1
BCB O1A   O  0 ? ? ? 1
BCB O2A   O  0 ? ? ? 1
BCB 'N B' N  0 ? ? ? 1
BCB C1B   C  0 ? ? ? 1
BCB C2B   C  0 ? ? ? 1
BCB C3B   C  0 ? ? ? 1
BCB C4B   C  0 ? ? ? 1
BCB CMB   C  0 ? ? ? 1

[download]

Results

P:\test>test1
BAZ|'N3''|N|0|?|?|?|1
BAZ|'N4''|N|0|?|?|?|1
BAZ|'C8''|C|0|?|?|?|1
BAZ|C9|C|0|?|?|?|1
BAZ|ZN|ZN|0|?|?|?|0
BAZ|HN1|H|0|?|?|?|1
BAZ|1HN2|H|0|?|?|?|0
BAZ|2HN2|H|0|?|?|?|0
001|F11|F|0|?|?|?|1
001|C11|C|0|?|?|?|1
001|O 1 1|O|0|?|?|?|1
001|N12|N|0|?|?|?|1
001|C12|C|0|?|?|?|1
001|C13|C|0|?|?|?|1
001|C 14|C|0|?|?|?|1
001|C15|C|0|?|?|?|1
001|C16|C|0|?|?|?|1
BCB|CBA|C|0|?|?|?|1
BCB|C  GA|C|0|?|?|?|1
BCB|O1A|O|0|?|?|?|1
BCB|O2A|O|0|?|?|?|1
BCB|'N B'|N|0|?|?|?|1
BCB|C1B|C|0|?|?|?|1
BCB|C2B|C|0|?|?|?|1
BCB|C3B|C|0|?|?|?|1
BCB|C4B|C|0|?|?|?|1
BCB|CMB|C|0|?|?|?|1
27

[download]
Examine what is said, not who speaks.
"Efficiency is intelligent laziness." -David Dunham
"Think for yourself!" - Abigail

In reply to Re: can't use unpack or split?? by BrowserUk
in thread can't use unpack or split?? by seaver

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.