cis safe mode

Hello,

I want to scan my external hard drive with cis. I want to scan my external hard drive in safe mode to prevent the autorun of the external hard drive in my pc. My question is: If I press right click and scan the external hard drive in safe mode will work the same if I did the same thing in normal enviroment? I mean the cis work in safe mode the same correctly as in normal enviroment?

Windows xp