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Microsoft Security Essentials (MSE) has been around for some time and has proved to be a popular, free anti-virus program. In this guide, I’ll show you how to configure MSE, what all the options mean, and some advanced tips to make the program run optimally for you.

Download MSE

If you still don’t have MSE or if you’re not using the latest version, you can download it here (I recommend you use Internet Explorer for the download.)

Basic Configuration of MSE

In this part of the guide, I’ll walk you through the basic configuration of MSE and explain what the settings mean and, in some cases, what the optimal settings are.

To get started, open MSE by double clicking on the MSE icon in the system tray.

Under the Update tab, click Update (if available.) MSE will now get the latest virus definitions so you are up to date with your protection:

Once downloaded, you should see the following message on the Home tab:

MSE Settings Tab

Now click the Settings tab and click Scheduled scan. You should run a scheduled scan by selecting Run a scheduled scan on my computer and picking a time when your computer is turned on but you are not using it. I have my scan run on my desktop at 2AM every Sunday. I also recommend you run a Full scan on this schedule.

Also, be sure to check Check for the latest spyware definitions before running a scheduled scan and check Start the scheduled scan only when my computer is on but not in use. The first of the two options will make sure you have the latest definitions and the second option will ensure that if you happen to be on your PC during the scheduled time, MSE won’t start the scan (as you will probably notice slow downs during the scan.)

Now click Default actions. I choose Recommended action for all four alert levels. If you’d like to learn more about actions and alert levels, go here.

Click Real-time protection. I highly recommend you use real-time protection, which monitors files as they appear on your PC (i.e. internet downloads, thumb drives etc.) Learn more about real-time protection here.

Click Excluded files & locations. Here you can specify files, folders, or drives where MSE should not scan. Possible exclusions could include:

  • Network drives monitored by other PC’s virus checking utilities.
  • Files, folders, and drives that are read-only (thus, they don’t change and should not pose a threat.)
  • Folders you are absolutely sure are safe and are not modified.

Personally, I recommend you leave this screen blank unless you have a good reason not to.

The same goes for Excluded file types and Excluded processes.

Click the Advanced tab:

  • Scan archive files:  (Recommended) i.e. zip filesI recommend you check as they are often used to house viruses.
  • Scan removable drives: (Recommended) If you use other people’s drives or if anyone has access to your USB ports, check this
  • Create a restore point: If you’re worried about MSE cleaning up important files, check this option
  • Allow all users to view the full History results: If you want your children to see you’ve been downloading questionable files (i.e. freepoker.exe… girls-screensaver.scr) packed with viruses, check this box. Joking aside, you’re almost done with configuration, so you can leave this unchecked if you’re not sure and want to move on with configuration…
  • Remove quarantined files after: Recommended if you don’t plan to manually clean up any quarantined files.
Note: There are performance trade-offs with each of these options. If you’d rather be safe than speedy, check all four.

Finally, click MAPS. Here, I opt for the Basic membership, which sends non-identifying information to Microsoft to help them improve MSE’s effectiveness in virus detection and removal. The advanced membership sends more detailed information to Microsoft about the virus and how it operates on your machine. It’s up to you which membership you use, but I chose Basic.

Finally, click Save Changes

Now You’re Set Up, Run a Full Scan

Now you’ve taken time to set up MSE, why not run a scan to make sure there is no malicious software on your PC?

Click the Home tab, under Scan options select Custom… and click Scan Now.

Chose the drives or folders you’d like to scan and click OK.

Take a break (or a nap if you have large hard drives) and let MSE do its job:

Advanced Tips and Tricks for MSE

Here are some tips and tricks to help you get even more out of MSE:

5 things you should know about MSE.

Scan a File for Viruses with MSE

With MSE, you can scan an individual file for malicious software. Learn how to scan a file for viruses with MSE.

Fix Issues with the MSE

If you are experiencing problems with MSE, you can use the Fix MSE Utility, which will reset all registry settings to their default values.

Update MSE with Windows Update Disabled

If you don’t use Windows Update (you really should for security purposes — but there are reasons not to i.e. Corporate network blocking, Viruses disabling Windows Update etc.), then you can use the MSE Update Utility.

Update MSE Offline

If you’re using MSE offline (i.e. on a computer that’s not connected to the internet), you can still update MSE:

  1. Download the latest definitions directly from Microsoft 32-bit | 64-bit
  2. Run the downloaded executable file, as an Administrator, on the PC that’s offline.

More instructions from Microsoft to update MSE offline.

What else do you do with MSE that could help others? What questions do you have about MSE? Let us know in the comments.

Updated June 18th, 2012.

2012/18/06 — Old beta and SpyNet references removed. Updated screenshots (where applicable) for version 4.0 of the client with details on MAPS. Updated broken Microsoft help links.

About Rich

Rich is the owner and creator of Windows Guides; he spends his time breaking things on his PC so he can write how-to guides to fix them.

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2 thoughts on “The Complete Guide to Protecting Your PC with Microsoft Security Essentials (MSE) [Updated]”

  1. Kennryanotarra says:

    even you disabled windows update still MSE updates.

  2. Rich says:

    Sadly, flowers are not an option :( I know… software just aint the same these days!

    So what are recommended actions? When you select Microsoft Security Essentials’ recommended action, this means that you want Microsoft Security Essentials to decide how to handle this alert level. Here’s how the program handles alerts, depending on their level:

    Severe or high level alerts : If Microsoft Security Essentials alerts you about potential threats that are severe or high, the recommended action is to remove these programs.

    Medium level alerts : For medium alerts, you should review the alert details (click the Show details link) to see why Microsoft Security Essentials detected the item. If you don’t like what the software does or if you don’t recognize and trust the publisher, consider blocking or removing the software.

    Low level alerts : This type of alert typically indicates a benign program, unless the program was installed without your knowledge or consent. If you’re not sure whether to allow the software, review the alert details, or check to see if you recognize and trust the software publisher.


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