just a heads-up, remember that the primary purpose of defragmenting your HDD is to speed up access times. it won't necessarily fix any problems, and could make things much worse so be careful!
defragging is not always a good thing, and it can mess things up completely if you have undetected disk errors -- always run
CHKDSK /R or SCANDISK first, and then maybe run DXDIAG and post the info pertaining to your OS and system specs so we can try to help further. good luck!
p.s. I believe Spybot detects the most common trojans, highly recommended program in any case.