One word: LUKS
LUKS is a full-disk encryption method. At boot-time, you have to enter a passphrase. With the given passphrase, a key slot is unlocked and the actual key for encrypting the data is retrieved. LUKS can be seen as a encrypted partition which holds another partition.
Because most users have multiple partitions (the
/ partition and swap), it's often used with LVM to avoid having to enter a password for each LUKS encrypted partition. LVM can be seen as a special partition holding multiple partitions (simplified). The structure would look like this:
Using the alternate CD, you can create a new installation using LVM + LUKS. Within the disk partitioning step, an option is visible for copying data from another partition. If you do not mind reinstalling the whole system, backup your files and settings and do a new installation using the alternate CD.
For a more correct documentation of LUKS (cryptsetup), see Cryptsetup FAQ.