How do I encrypt file system on Linux (/). I know, how to do that on fresh installation, but how to achieve same, when Linux is already installed? Can i move everything from main partition to secondary (which is encrypted) and somehow change / mount point?
Yes, you can.
Essentially it is the same process as moving a Linux install to a new disk/partition, only the new partition is encrypted.
Only caveat: As the new system needs to boot from an encrypted /, you need an additional, unencrypted /boot so the system can boot. Also, the boot scripts need to support this configuration; current Debian/Ubuntu already does.
Edit: BTW, though this should go without saying, make sure you have a working and current backup before doing this.
Unsure if you would be willing to use a third party program to do this but if you are True Crypt is available for linux and is pretty good at encrypting the system drive. I have done so on numerous laptops here at work and use it on a multi boot system at home. They have just released a new version as well which I believe can spped up the encryption time as well.