About the only way to completely protect your .flv files is to not put them on the CD.
Or, only give CD access to authorized people.
But if this CD is for distribution, then as soon as someone else gets the CD, they already have a copy of the .flv files. So even if you were somehow able to super encrypt the files.... which the user would still have to de-crypt to view...all it takes is a simple screen capture to perfectly copy the video files.
So if the .flv files are intended for distribution, perhaps a better method would be to watermark each video and be sure to include a copyright notice in each one.
That being said, here is some info on Digital Media Rights management.
Perhaps you can glean something from that.
my CD will be distributed to the documentation center in the medical college where I study, and of course students and teachers will be able to use the CD and copy it.
is there a way to insert the videos in flash without having them on the CD? (like psd files, pictures etc.)
and how can I watermark each video? should I use some software for this?
Well the best feature of having all the content on the CD is that it's all self contained, no need to go someplace else (like the Internet) to get content. But it certainly is possible to store the .flv files on a Web server and have Flash content on the CD go to the Internet to download and play the videos. Little more complex to get it all working AND then the user must have an Internet connection available or they can't see the videos. But even then... if it's on the Internet it can be copied.
Or look into sone type of encryption program:
but I'm not sure that you can use the content without first decrypting the data.
As for watermarking and adding a copyright notice, this is normally done when the video is first being edited in whatever software is used to capture and edit the original video file. Once the file is already created, there are software programs to add the mark... something like this:
Best of luck!