In short, FDE would be an issue you would want to address during the install. If your partitioning schema uses LVS you could set up an encrypted volume using LUKS and copy system files to it, and reassign mount points in your /etc/fstab file, but this is ill advised, and very likely error-prone.
Now that your install is already 'mature' (in the sense that it's already installed and broken in), you might be better off concentrating on encrypting your home folder instead. For such operations you might look into cryptsetup or encryptfs. With full-disk encryption, a running machine is already in the auth'ed environment, whereas home folder encryption at least has the benefit of keeping the volume in question encrypted as long as the user isn't logged in.
But in summary, your best option to look into if still wanting full disk encryption (or at least partition encryption at this point in your install's maturity) would be LUKS.