I am trying to scan a system for virus and other stuff and its flagging me down to free up some system memory to get the job done. I went into task manager and began to end some processes and after a reboot they are still there.
So what am I doing wrong ?

Some malware will give you an alert like this, but it isn't real. Does the pop-up alert want you to click on it or to do anything else? Does it actually stop you from doing anything? If not, ignore it and keep on keepin'on. Are you in Safe Mode?