Using <FH> only gives you the first line where you want to get the whole file's content. This works:

use Crypt::SMIME;

open(PKEY, "signer_key.pem") || die "open failed: $!";
open(CERT, "signer.pem") || die "open failed: $!";

my $plain = <<'EOF';
From: alice@example.org
To: bob@example.com
Subject: Crypt::SMIME test

This is a test mail. Please ignore...
EOF

($privkey, $cert); # = (<PKEY>, <CERT>);
{
local $/=undef;
$privkey = <PKEY>;
$cert = <CERT>;
}

my $smime = Crypt::SMIME->new();
$smime->setPrivateKey($privkey, $cert);
# $smime->setPublicKey([$icacert]); # if need be.

my $signed = $smime->sign($plain);
print $signed;
[download]