BitDefender is a popular antivirus tool. And it also have a online version of its Antivirus that you can use to scan your system. it can scan your files, drives and boot sectors. If you already have an Antivirus in your system, you can still use this to scan your system.
ESET is a popular security company that has popular Antivirus Nod 32. It also has an online virus scanner that can help you in scanning different kind of security threats in your system. It is available for free. It only downloads a small piece of tool and then download virus database. After this it scans your whole system.
Trend Micro is another nice online virus scanner to help you in removing system threats. Trend Micro scans for various system vulnerabilities and and fixes them to prevent re-infestation.