A few days back i had a Trojan on my computer which i deleted but ever since then my computer got slow so i went to taskmanager to see what the problem was and I noticed chkdsk.exe takes up a lot of CPU memory which makes everything slow this did'nt happen before so i'm wondering if it's corrupted?

What Tojan was removed from the system and using what removal tool?

There were two types of trojans: Trojan Horse IRC/Backdoor.Sdbot2.LCK and Trojan Horse Downloader and i used AVG Free Edition to remove them.

Also i just did a scan and the trojans are back any tips on what to do?

http://vil.nai.com/stinger go to that address install Stinger, it should be able to remove both the trojans ...

Also, check to see if you have a file called "ms.exe" in your system32 folder.