[HOWTO] Run a Deep Scan for Malware

Category: Anti-Virus

A reader asks: 'My anti-virus software offers me an option to run a quick scan or a full scan. I've always run the quick scan, because that's the recommended setting. What does a full scan do, and how would I know if I need to do one?' Read on to learn about deep scanning, to check every nook and cranny of your computer for malware...

What is a Deep AntiVirus Scan?

As you've noticed, the "quick scan" option is the default in almost every anti-virus and anti-malware software. A quick scan examines only the most common spyware hiding places, such as the Windows system folders, your Documents and Settings folder, and the registry.

A deep scan, sometimes referred to as a "full scan", "complete system scan", or "whole computer scan" examines every bit of your computer's RAM memory, hard drives, and removable drives. A deep scan will also scan your startup programs and the Windows registry for any traces of malware.

Malware (viruses, spyware and other nasties) usually comes in the form of an EXE or DLL file, but it can also hide in a JPG file (graphics image), a DOC file (Microsoft Word), a PDF, and many other places you wouldn't expect. If a virus or rootkit is lurking anywhere on your hard drive, external drive, flash drive, or on a CD/DVD disk, a deep scan should find it.

Antivirus Deep Scan

Because it must open and scan through every file on every drive, a full scan will take a lot longer than a quick scan. You should set aside at least two hours to allow a full system scan to complete. You can continue to work while the scan is in progress, but performance will probably take a significant hit due to the disk-intensive scanning operation.

How often should you run a full or deep scan? Most experts agree that a scheduled quick scan will do a good job of protecting you, if run on a daily basis, along with real-time malware detection. These are standard features for almost all anti-virus software, even the free versions. I would definitely recommend a full scan if you suspect that your system is infected. Beyond that, a full scan once a month seems more than sufficient. If you're paranoid, or just have CPU cycles to burn late at night, schedule a deep scan to run weekly.

How to Start a Full Scan

There are many different anti-virus programs available, so it's not always obvious how to initiate a full anti-virus scan, and which options are important. Below are step-by-step instructions for deep scanning with the most popular free anti-virus programs. Click the desktop icon or the mini-icon in the task bar to open your program's main menu, then jump to the appropriate set of instructions. If you don't have an anti-virus program yet, or you want to check into free alternatives to the paid security software you now have, see my related article on Free Anti-Virus Programs before continuing.

Avast Free - Full Scan

  • On the Avast main menu: click "Protection"
  • Click the "Scans" option
  • Under "Full Virus Scan", click "Settings"
  • Under "Scan Areas" select "All harddisks", "All removable media", "Rootkits (full scan)", and "Auto-start programs and modules loaded in memory".
  • Select the "content" radio button under "Recognize file types by"
  • Check the box next to "Scan all files"
  • Click OK to save settings
  • Click "Full Virus Scan" to run the scan.

AVG Free - Full Scan

  • On the AVG main menu: click the gear icon next to the green "SCAN COMPUTER" button
  • Click the gear icon next to the "Deep Scan" option
  • Under "Full Virus Scan", click "Settings"
  • Under "Scan Areas" select "All harddisks", "All removable media", "Rootkits (full scan)", and "Auto-start programs and modules loaded in memory".
  • Select the "content" radio button under "Recognize file types by"
  • Check the box next to "Scan all files"
  • Click OK to save settings
  • Click "Deep Scan" to run the scan.

You might have noticed that the instructions for deep scan with Avast and AVG are almost identical. That's because AVG was purchased by Avast in 2017.

Avira Free - Full Scan

  • On the Avira main menu: click "Open" on the line that says "Antivirus"
  • Click the "Scan" icon
  • Select "Full Scan"
  • Select "Start Scan"

MalwareBytes Anti-Malware - Full Scan

In addition to the full scan option in your antivirus program, I recommend that you download the free MalwareBytes Anti-Malware (MBAM) program and run the full scan option in this program as well. MBAM scans for all types of malware (not just viruses) and sometimes finds things that are not detected by other anti-virus scanners. MBAM makes it easy:

  • On the MBAM main menu: click the "Scan" button
  • Select the "Custom Scan" option and click the "Configure Scan" button.
  • Under "Custom Scan" options check all the boxes
  • Select the disk drive(s) you want to scan.
  • Click "Scan Now" to start the scan

Windows Defender Offline - Full Scan

If you are not able to start your computer due to a malware infection, the Windows Defender Offline (WDO) is a stand-alone deep scan utility that runs from a bootable CD or USB flash drive. You can also use WDO as an adjunct to the full scan option of your installed anti-virus software.

Too Much of a Good Thing

Let me repeat a caution here that I've mentioned before. It's okay to run a dedicated anti-virus program along with an on-demand scanner such as MBAM. But I strongly advise that you run only ONE dedicated anti-virus program at a time. If you run two or more, the real-time virus detection engines can actually fight with each other. Each will think the other is an attacking virus, and the ensuing battle for supremacy can bring your system to a crawl.

I actually tested this once on a Windows 7 system. After installing Microsoft Security Essentials, Avira, and Avast, my system came to what seemed like a complete halt. I hit the power button to reboot, and 20 minutes later it was still cranking away. Trying to open any program or navigate the web was like swimming in wet cement. If you want to install a second antivirus program to run a "second look" scan, be sure to use the option to disable real-time protection in the first one.

Do you have something to say about running a deep antivirus scan? Post your comment or question below...

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Most recent comments on "[HOWTO] Run a Deep Scan for Malware"

Posted by:

16 Mar 2018

2 hours for a full scan ?
I only have a 500 gig hard drive and it is only about 180 gigs used.
If I run a full scan using Malwarebytes and check all the boxes in a custom scan, it takes a full day.
Using Defender it takes half a day.
My laptop is pretty swift in all activities except those I listed.

Posted by:

16 Mar 2018

I have used Malwarebytes Free for a good while, a few years or more. I highly recommend it. Very easy to use. I upgraded to Malwarebytes Premium after running the 14 day free trial. I love it! I was reading your site just a few minutes ago and MB threw up a warning at a add I clicked on on your site. I VERY highly recommend MB Premium.

Posted by:

16 Mar 2018

I have been using PC Matic, you've prop seen their commercials on TV...American Made, American Support. Do you ever compare them to other programs? I usually get an answer to a virus question within 24 hours. Try that with Norton or McAfee. Anyway whats your research on PC Matic?

Posted by:

16 Mar 2018

I use IObit's "Advance System Care Ultimate 11" and just finished a Full Scan several hours ago. It took 8-hours and found a "trojan" virus on a downloaded form. I only run it once/twice every couple of months. I am usually virus-free. I was surprised at the latest catch; but happy to see it was caught. I also use IObit Malwarebytes. This program scans automatically every day (at least that how it seems to me), and the results are always "clean." Like Jack, what's your research on IObit products, Bob?

Posted by:

16 Mar 2018

Hi, I use MBAM, AVAST and a program called HerdProtect.
Herdprotect is an ON demand scanner which scans your computer with 60+ anti-virus engines.

Just putting in my penny's worth

Posted by:

17 Mar 2018

Hi Bob, I read,and most of the time follow your advice. Like Jack in this comments posting, I also use PC Matic and wonder why you never acknowledge them? They are absolutely great in cleaning my machine and also a great antivirus. Why don't you share your opinion? Don't be afraid to try them.

Posted by:

Bill d
17 Mar 2018

In your article on "How to Run a Deep Scan" you mention the importance of not installing two, separate virus scan programs on your computer. In the same article you recommend downloading and choosing the full scan option of Malwarebytes. Is it OK for Malwarebytes to run along with another anti virus program without causing the problems you describe in the article?

Posted by:

18 Mar 2018

Respectful wishes for the 17th of March.

Posted by:

18 Mar 2018

hello ...

first..bill d
you can run MB and your antivirus..Im not a tech but out of many years of being on a computer, early on when I realized I couldn't afford to have a professional tech, I was fortunate enough to come across a computer message board (early form of a forum)..real early! I became friendly with a guy who was a professional tech...he was so heloful, that I was able to build my own computer...

In my"early" years, I came across and loved ZoneAlarm, used them for many years, but eventually it to me became garbage, like most others if that period... next I used AVG,Avast and yes when Norton, etc.
For me they all became huge resource hogs... Eventually out of frustration I have Windows Essential.. but along with that always used MB.. but I would about once a month an online scanner from TrendMicro Housecall
But cane across PC Matic...must say that these all kept me safe through the years.

But...I would like to add...that receiving a newsletter such as this one, Windows Secrets, etc are
VERY IMPORTANT! For if it wasn't for them, info like this
you wouldn't even think about what goes on with your own computer, laptop, Pads and phones.
So huge Thank You to
Bob Rankin and those like him!

Posted by:

19 Mar 2018

Dr. Bob: Avast did a full scan 4 me in less than 30 minutes. However, MBAM does not show "custom" scan. I find that the "current" v. is where the MBAM website shows it to be v. 3.4.4. (as of Mar. 6 2018). (I have sent a support request to MBAM since their Chat Line is not in service at this time.

MBAM also "blocks" your newsletters from time to time. I used to swear *by* at MBAM but am beginning to think I need to start swearing *at* MBAM.

I have the Premium version and have used it for several years.

Posted by:

Gary in wisconsin
21 Mar 2018

MSE, PC Matic, I use IE 11 and I refill my own ink tanks....... YMMV!

Posted by:

16 Apr 2018

Hi Butch, I see that you stated that the latest version is 3.3.1 Can I update you that the latest version was released on the 29th March 2018 to version 3.4.5

Posted by:

02 Jan 2019

May you all enjoy a peaceful, happy and contented 2019 with no computer glitches.
I have been using PCMatic daily for many years and it has found 2 that it deleted, both downloaded by Microsoft. Also use Microsoft Security daily.
In that time I did notice you once highly recommended this program as I do..... Bob

Posted by:

18 Jan 2019

I have three times followed the directions for the AVAST full scan--or so I thought. No "OK" appears; thus, I'm not able to save the settings or able to click the Full Virus Scan. Any idea what I'm not doing that I should have done or that I might have done that I shouldn't? "OK" is nowhere to be found.

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