We don't recommend safe mode for Malwarebytes scanning because some things will not load in safe mode and Malwarebytes needs to be able to look at running processes so it can identify the bad ones. (this is how it identifies Root Kit infections)
It can be run in safe mode if the computer is so badly infected that Malwarebytes won't run in normal mode though, and then once partially cleaned another full scan in normal mode is recommended.
