The headers are divided from the body by a empty line (an array element containing just "\n").

$msg = $pop3->get($msgnum);
# strip header
1 while shift(@$msg) ne "\n";
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But, depending on what all you are doing with the message, you may want to use a module to parse the message:

$msglines = $pop3->get($msgnum) or ...;
$msg = Mail::Internet->new($msglines) or ...;
$body = $msg->body;
for my $linenum (1..@$body) {
   print "Body line $linenum: $body->[$linenum]\n";
}
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