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By identifying the class of the Trojan you are infected with and visiting the website of your favorite virus scanner, you can find step-by-step instructions on how to manually clean your registry entries and correct other configuration changes made to your machine.
However, once you are infected and depending on how long you've been infected, the intruder may have made even more modifications to your computer manually and that makes it hard to detect and even harder to be absolutely sure if you are completely clean. Because of this, sometimes you'll have to be prepared to do a clean format if your computer has valuable information or if it's a mission critical machine.
Remember to be proactive. Running a good virus scanner and firewall is always an easier task than cleaning a virus or Trojan.