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.
Note: This guide is written for those using the stable release of MSE; however, if you’d like to download the Beta, get it here.
Download MSE
If you still don’t have MSE, you can download it here.
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 processes. If you know processes that should be excluded, you probably don’t need to read this part of the guide (and you can definitely teach me a thing or two!)
Click the Advanced tab. I recommend you check Scan archive files i.e. zip files as they are some of the most common files to contain viruses (in the files that are stored in the archive.) The next three options are up to you and you can see my configuration below. I disable reading of USB thumb drives on my computer so I don’t need to scan them but you may want to check this one.

Finally, click Microsoft SpyNet. 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.

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.
Download the Beta
If you want the latest version of Microsoft Security Essentials, be sure to get the Beta version of MSE here.
What’s new with the beta? From the Microsoft Connect site:
- Windows® Firewall integration: Microsoft Security Essentials setup allows you to turn on Windows Firewall.
- Enhanced protection from web-based threats: Microsoft Security Essentials has enhanced integration with Internet Explorer® which helps prevent malicious scripts from running and provides improved protection against web based attacks.
- New and improved protection engine: The updated engine offers enhanced detection and cleanup capabilities and better performance.
Fix Issues with the Beta Version
If you have installed the latest beta of Microsoft Security Essentials, you may find it doesn’t work as expected. Download the Microsoft Security Essentials Restore Tool to get everything running smoothly again.
Fix Issues with the Stable Release
If you are experiencing problems with the stable release of MSE, you can use the Fix MSE Utility, which will reset all registry settings to their default values (which should restore order to your copy of MSE.)
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:
- Download the latest definitions directly from Microsoft 32-bit | 64-bit
- Run the downloaded exe, 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.
Search Windows Guides