well, the linked article above is from 1998, there are some better solutions today
If you wanna encrypt your whole filesystem I'd recommend to use an encrypted lvm with (at least) 3 logical volumes (/, /home and swap). For encryption use dm_crypt. The debian installer offers this in it's partition dialog, certainly other distibutions have solutions as well.
You don't need to re-install linux of course. I have only my /home and swap encrypted and copied+symlinked /var and /tmp to /home. I'd suggest you read some tut's and then ask again if you have more specific questions.
Alternatives to dm_crypt would be truecrypt and loop-aes.