step 6. Test it! - it was necessary to add a small fix:

#/usr/bin/perl

use strict;
use warnings;

my $string_original  =<< "END";
("Immunologic and Biological Factors"[MESH] OR "Immunosuppressive Agen
+ts"[MESH] OR "Transplantation Immunology"[MESH] OR "Allergy and Immun
+ology"[MESH] OR "Graft vs Host Disease"[MESH]) NOT ("Foo"[MESH] OR "B
+ar"[MESH]) AND ("Kidney Transplantation"[MESH] OR "Liver Transplantat
+ion"[MESH] OR "Heart Transplantation"[MESH]) NOT ("My Term"[MESH] OR 
+"Blah"[MESH]) NOT "foobar"[MESH]
END

# original

{
my $string = $string_original;

$string =~ s/ NOT ".*?"\[MESH\] ?//g;
$string =~ s/ NOT \(.*?\) ?//g;

print $string, "\n";
}

# Corion's

{
my $string = $string_original;

$string =~ s! NOT (?:".*?"\[MESH\]|\(.*?\)) ?!!g;

print $string, "\n";
}

# fixed

{
my $string = $string_original;

$string =~ s! ?NOT (?:".*?"\[MESH\]|\(.*?\)) ?!!g;

print $string, "\n";
}
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