If you believe that your computer may be infected, you will probably want to run a full malware scan while in safe mode. Safe mode has the benefit of stopping many malware programs from running and interfering with your scan. Malwarebytes is able to run in safe mode, but it may take a little work.
Benefits and Negatives of Safe Mode
Safe mode is a special boot option that comes in quite useful when trying to cure your computer of various malware infections. Safe mode basically just runs a stripped down version of the operating system. Most of the drivers are turned off and a number of features aren't accessible, but this means that a number of malware programs won't be able to run their processes either. If you fear that malware infections on your computer are interfering with your antivirus programs, you can use safe mode to run a clean scan.
That said, it isn't a cure all. Safe mode is fairly stripped down, so you may not be able to fully run some virus scanners. Malwarebytes can run normally, but there is a concern that some features won't be able to run fully. Safe mode also might not completely shut down the malware, or it may just be a temporary cure. If you don't wipe out all traces of the infection, there's a chance that it will just reinstall itself from the scraps when you boot normally.
Preparing a Malwarebytes Safe Mode Scan
If you don't already have Malwarebytes installed, then you will need to install it.
Just go to Malwarebytes.org and use their download link to get the installer from one of their verified mirrors. If you can, just stick to a normal installation. Unfortunately, if you're suffering from a fairly serious infection, Malwarebytes might not install. If you're having trouble with Malwarebytes installing, we have a full article on how to troubleshoot your Malwarebytes installation. In short, you can use a few other mirrors, or simply rename the installer to stop the usual bunch of malware from blocking it.
If you can't install it at all, then you can try to install it while in safe mode. You just need to make sure that you use safe mode with networking, so that you can update it after the installation. There are other methods for manual Malwarebytes updates, if you're having trouble.
Once Malwarebytes is installed, you're actually ready to go.
How to Run a Malwarebytes Safe Mode Scan
You can run a Malwarebytes safe mode scan quite easily. For the most part, you should just be able to boot into safe mode by hitting "F8" while your computer starts up. This linked article on reaching safe mode in Windows 7 covers the basics well and offers a few alternatives methods if malware is blocking your computer from using safe mode normally.
Once you manage to reach safe mode, you should be able to just use Malwarebytes normally. Run a full scan (this will probably take a while, so have plans to kill time for a few hours). After the scan runs, it should find and remove the malware on your system. Follow the on screen instructions and finish the removal, then boot your computer normally. You should probably run a scan again in normal mode to make sure that you go anything.
This should hopefully take care of most infections though. If you would to learn more about using antivirus scans in safe mode, the linked article covers all of your options for scanners and a few tips and tricks for general safe mode virus removal.