$re = '/(?=(?!^)[^\[\]]*?\[|[^\[\]]+$)/m';
$str = 'ABCDE[NOT]FGH
CCGF[NOT]HI
MPJ[NOT]L
MNA[NOT]PLJ[KAJ]SHD
MPJ[NOT]
[NOT]L
MNA[NOT]PLJ[KAJ]SHDMNA[NOT]PLJ[KAJ]SHDMNA[NOT]PLJ[KAJ]
MNA[NOT]PLJ[KAJ]SHDMNA[NOT]PLJ[KAJ]SHDMNA[NOT][KAJ]';
$subst = " ";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php