Be warned: Any malware on your system- be it a trojan, worm, virus, or other code can be nearly impossible to get rid of if you are already infected.

I would start by preventing everything from loading into the startup session. The best way to do this is using a little known tool called "msconfig". Here is what you do:

Start > run
Type: 'msconfig' then enter.

When you have msconfig up, click on the last tab on the right, 'startup' and uncheck everything you see there. These are the items that are loading everytime your pc starts up. By unchecking these programs/processes, you are in effect keeping them from starting up with your machine when you boot.

Once you have disabled all the startup items, go download a tool/program called "Spybot Search & Destroy" and install it.
The home of Spybot-S&D!

Once you have installed Spybot, run all the updates and scan your machine. It won't get rid of everything, but it will hopefully get rid of the simple malware you may have on you machine.

To be 100% sure, you may have to reimage your pc. I know it's a pain in the ass, but it may the the only way to ensure you have gotten rid of everything. I myself never would trust a computer which was infected in the first place, no matter how much "cleaning" I tried to do. Trojans are very dangerous and can expose you to risks (like password gathering & keylogging) that will drive you nuts.