use strict;
use warnings;

my $text = join q{}, <DATA>;
my $newtext = q{};

while ($text =~ m{
  \G              # start where we left 
  (.*?)           # text to be mangled
  (?:             # followed by
    STARTPATTERN  # the start of verbatim mark
    (.*?)         # the text to be taken verbatim
    ENDPATTERN    # the end of verbatim mark
  )?              # must not be always present
}xmsg) {

  # add the mangled version of the text
  $newtext .= mangle($1);

  if (defined $2)
  {
    # if there is a verbatim part, copy it verbatim
    $newtext .= $2;
  }
}
print $newtext;
exit 0;

sub mangle
{
	return uc $_[0];
}
__DATA__

Once upon STARTPATTERNa timeENDPATTERN there 
was a Perl monk. STARTPATTERNBy steadily trainingENDPATTERN 
the great virtues he became very wise...

##</code><code>##

ONCE UPON a time THERE 
WAS A PERL MONK. By steadily training 
THE GREAT VIRTUES HE BECAME VERY WISE...