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I use the free AntiVir anti-virus program from Avira. When I installed it I ran a full system scan. should I run the full system scan again in the future even if AntiVir is set to Auto Protect on.

Or is there no need to run "full system scan" again if I'm updating virus definitions regularly (auto update).

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Ask yourself these questions: What harm would it do? What good might it do? – Bryan Mar 2 '10 at 7:38
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Technically no - but yes you should!

Basically, the reason for yes is that it is simply best practice - any form of malware could infect your machine inbetween updates (e.g. 0-day outbreak) and be on your machine. Scanning your computer will check your hard drive against the latest signatures and simply ensure that you are protected.

However, I also said technically no - A virus cannot do any damage simply by being there, it needs to be executed. But, you would also need to understand how it got there in the first place.

You could've been infected by a 0-day type exploit in Acrobat, Flash, Java or other which executed - not being detected by the scanner and then left a few files, technically harmless but still part of that virus - or it could leave something such as a scheduled task to be executed at a later date.

However, when you do update your scanner, it should be able to detect any active processes that previously snuck past it if it is still running and also detect any part of the malware (e.g. if it left a scheduled task or a .dll loaded in to Windows). But, if it did manage to get on your system in the first place, technically it could also have installed a rootkit or other bypass mechanisms.

Anyway - it most likely will come up with nothing (other than possible tracking cookies or other harmless stuff depending on the scanner) but there is no harm in scanning - personally, I would leave it as a scheduled task.

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It is 7:21AM, my body clock is messed up - I have been up ALL night working on a project. If this is not easy to read, I am sorry (I'm not that good at best of times, let alone when tired!), please say here and I will try to rephrase/correct anything when I am more awake! – William Hilsum Mar 2 '10 at 7:22
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Yes, you should scan your computer periodically, and by more than one such product, because new viruses are discovered each day. It's theoretically possible that the virus you're infected with hasn't yet been added to AV's database. Also, not all antivirus products use the same virus database or the same virus detection-methods.

You should also use some anti-advertisement product such as Spybot S&D or Lavasoft Ad-Aware, because antiviruses do not find everything.

You should keep in mind that having your computer declared as clean by any antivirus product, does not really guarantee that it's clean.

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but when i run full system scan first time there was no virus and after that my software's is auto updating definition whenever available on company's server and software Runtime detection (auto protect) is also on. – metal gear solid Mar 2 '10 at 7:32
@Jitendra vyas: Runtime detection is not foolproof, and in any case won't detect files that are not being executed. Runtime detection walks the line between full protection and slowing the computer to the point of being unusable. AV programs themselves are continually evolving to detect new threats and attack vectors. When an antivirus labels the computer as 100% safe, it makes one feel better, but it doesn't mean that it's not in fact infected by a virus that's (currently) not tested by this AV. – harrymc Mar 2 '10 at 9:17
And it also doesn't mean that you're not going to be infected 5 minutes later, by a website using a propagation method unknown to Runtime detection. – harrymc Mar 2 '10 at 9:21
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