$ cat file
*start*of*junk*data*this is all junk data 01*end*of*junk*data*binary data binary data binary data
*start*of*junk*data*this is all junk data 02*end*of*junk*data*binary data binary data binary data
*start*of*junk*data*this is all junk data 03*end*of*junk*data*binary data binary data binary data
*start*of*junk*data*this is all junk data 04*end*of*junk*data*binary data binary data binary data

##</code><code>##

#!/usr/bin/perl -w
use strict;

my $file="file";

open FILE, $file or die $!;

while (<FILE>) {
  if (m{"*end*of*junk*data*".*?}i .. m{"*start*of*junk*data*".*?}) { print; }
}

close (FILE);