If you need to check only one folder or file, right-click it and select Scan with Microsoft Security Essentials from the menu.
If nothing is found, Microsoft Security Essentials window opens with green status. You can then close the window.
In case something malicious is detected, Microsoft Security Essentials window opens with red or yellow-orange status (depending on alert level) and a large Clean PC button. If you've configured MSE to apply automatic actions, the cleaning process might have already started.
After cleaning is complete, Microsoft Security Essentials turns its status to green. Click Close and then close main program window. In some cases, a restart is required to remove a bit nastier malware.
Running a monthly full anti-virus scan with Microsoft Security Essentials
A full scan should be performed once every month to ensure that there are no viruses and malware hiding somewhere deep in your computer. You should also run a full virus scan when status of Microsoft Security Essentials remains red after a quick scan.
Open Microsoft Security Essentials by clicking on its fortress icon in Taskbar Notification Area/System Tray. You can also right-click the icon, that makes no difference. Then click Open.
Microsoft Security Essentials main window opens. Make sure Home tab is open. In the right part of the window click Full under Scan Options. Then click Scan now.
Wait until the scan is complete (this might take several hours). Well, you can do some work if you have a fast computer, or you can call your friends or do some exercise... 
If everything's fine, you can safely close MSE window.
If something malicious has been detected, Microsoft Security Essentials will turn its status to red or yellow-orange and present a big button named Clean PC after the scan is complete. Click that button. If you've configured MSE to apply automatic actions, the cleaning process might have already started.
Microsoft Security Essentials will then quarantine or delete the item and present a success message. Click Close. In some cases, a restart is required to remove all traces of malicious software.
