How to protect myself if i am using ktorrent or transmission
 

As above .

Protect from what?

Your question is very vague. What do you need protection from?
Viruses? There are not that many viruses for Linux. So chances are slim that you will catch one from downloading with *torrent. To be safer you can scan downloaded files with clamAV (or any other Antivirus program) afterward.

Or do you mean protection from being detected and prosecuted for downloading copyrighted material? In this case there is a *foolproof* and very effective measure you can take:
Do not illegally download copyrighted material!

Hope this answers your question.

If you are implying something like PeerGuardian's IP filter, this lists instructions. (I have not checked them, so no idea whether they work or not). Anyway, AFAIK, IP filters is possible in most torrent applications. But, I second crts that if you want to "protect yourself" while downloading torrents, make sure that you don't download any illegal ones.

protect from WHAT ???
a MS windows virus
then do not copy downloads to a windows box

from the MPAA suing you --- have fun with that
- it is against form rules for us to tell you how to do something that IS ILLEGAL

Uninstall them so you are not tempted to use them.

simple, don't download content that will attract the attention of the copyright holders, or better yet, don't download copyrighted material at all, it's a proceed at your own risk business.

if you are torrenting a linux iso for instantce, nobody is gonna care, probably the same goes with movies and music from the 1940s('50s) (1923 for sure) and prior where the copyright has probably long ago expired and are now public domain.