There are several kinds of Trojans, and each may have a different effect on your machine. Trojans are mostly recognized by most up-to-date virus scanners. However, once the Trojan is executed, it will make several changes to your registry and configuration which are not easily detected by virus scanners and can't be cleaned automatically. That's when an anti-Trojan program may do a better job in cleaning your computer.

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.