Hi,
If certificate is already uploaded in APIC-EM, you can export certificate via your browser.
Chrome:
Open console with F12 > Security tab > click on View certificate > Details tab > Copy to file... > Next > Choose format > Next > Browse > Choose location to store
If you want get list of all certs in APIC-EM controller, use SSH (user 'grapevine', IP address that you specified using configuration wizard for the network adapter). After login, change directory to /etc/grapevine/.pki/openssl/certs/ and there are stored related .pem files.