Popups and Mcafee

Mcafee is a Anti-virus program, with other abilities, depending on the version. It doesn't do as good a job at detecting and removing malware, which is a separate kind of infection, designed more to annoy and advertise, then spread and damage the computer. Also, it can only protect you so much. Think of it like a seatbelt, protects while your driving, but if you get into a serious enough accident, it won't be that much help. 

First thing to do is figure out what kind of infection it is. Could you describe the popups? Are they all different or do they share a common theme? Do they ask you to do anything? Do you notice any new icons in your task tray, thats on the bottom right of screen next to the time. Or any errors when you reboot, something like "Such&such failed to respond, would you like to close it anyway?" These are all clues. But there is no easy answer. How you get rid of the thing depends on what it is, and how dug into your computer it is. Hopefully I will be able to help more once you reply with a bit more info. Thanks.