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taking by the hand.....
First,
Unplug yourself from the net, then noone can intrude, and all imminent danger is gone.
Second,
Find out which trojan it is. If you find ziltch on the HDD, take a look at the running proccesses.
Third,
Even a trojan needs a way to start itself. Take a look at http://www.tlsecurity.net/auto.html to find out how. Then delete every option you find beeing used, thus disabling it's capability to run itself.
Fourth,
Get yourself a decent virus-scan and let it run *ALLWAYS*
Fifth,
if you're still nowhere, place your nice install CD in the cr-rom drive and reboot the frigging thing.
Grtz,
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Download and install zonealarm and that will keep unathorized access to your computer and block trojans from coming in and out of your computer.