SuperAntiSpyware
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Before you run a scan in SuperAntiSpyware you should always update your definitions for the program so that it can effectively find any new strains of infections that may not have existed since you last ran a scan. Use the Check For Updates button on the bottom left to do this. Always continue to do updates until the application tells you that there are no more updates to download or install.

Scanning is very simple, just select the Scan Your Computer button then select the drives and type of scan you would like to perform. Your first scan should be the Quick Scan because if you are attempting to get your computer back from the infections you will still need to run other malware / AV / Spyware complete scans at another time or all at the same time, but for now we are working on just getting control. After the scan is complete you will need to tell SuperAntiSpyware to remove the infections.

What I often suggest is to run a Quick Scan once a week and a Complete Scan once a month. This will go a long way to help keep you uninfected. You should do this with each program that you use to protect yourself from threats. Remember the difference between the free version and the paid version is having the ability to automatically run scans  without user intervention and the ability to catch the infections BEFORE they can attack your computer. All worth the price of the lifetime subscription to have piece of mind without having to do the work yourself.

 SuperAntiSpyware
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Now this selection can really help you. If you disable the "Enable First Chance Prevention" your computer will startup and shutdown much faster than if it was enabled; which is the default. Your system can be misarably slow on start-up and shutdown with this option checked. Of course you should check to see which of the three options or combinations of the three you can tolerate before just shutting them all down. This option is only available in the paid version.