If malware has taken ahold of your computer, you may not be able to boot up your computer. In this case, you can enter into the WIndows Recovery Environment. From here you can add and remove files, change the startup process, and attempt to fix problems before the system starts.
To get in the Windows Recovery Environment in Windows 7, you would boot from installation media or as the system is booting up press the F8 key to bring up the Advanced Boot Menu. From there, choose the System Recovery Options and select Command Prompt.
In Windows 8/8.1/10, you would boot from installation media and choose Troubleshoot > Advanced Options > Command Prompt.
From the Command Prompt, you can perform the actions needed to remove the malware or assist in getting your system booted properly.