You can get specific certificates for each FQDN such as ftp.mydomain.com and
www.mydomain.com. Once you have the certificates you can apply them to anything that answers as those FQDNs.
You can also get global certificates such as *.mydomain.com and apply to any server that answered any FQDN that ends in .mydomain.com such as ftp.mydomain.com,
www.mydomain.com, billybob.mydomain.com etc... Such certificates usually cost a lot more than specific ones so you would usually only want them if you were doing several in the same domain. Also the global certificates don't satisfy the requirements most browser have for showing the green security seal near the URL bar but they will see it as secure.