CPU and Memory running very high - please help!

A few days ago, I get this little Windows pop-up on my taskbar saying that my computer is unprotected and has been infected with a trojan (couldn't remember if it said which one exactly but I believe it said Alureon?). Afterward, my computer has been running very slow and the CPU/Memory widget I have pinned on my desktop shows they are pretty much maxed out, all the time, even while not having Internet Explorer or programs open (none that I have knowingly opened myself, anyway). I went out and bought McAfee Anti-Virus 2013 yesterday hoping this would resolve the problem. It did find 10 trojans and removed/quarantined them, but nothing has changed as far as system performance goes; everything still runs slowly, and opening even the smallest of programs like a calculator takes at least a few seconds.

I apologize if this thread is in the wrong forum and if I can be more descript, but I am more than willing to answer any questions or take screenshots if needed. Thanks so much for anyone's help concerning this matter!

P.S. - My computer isn't a beast by any means (Toshiba Satellite C655 running Windows 7 Home Premium 64-bit, 2 GBs RAM, Intel Celeron 2.2 GHz - was an Xmas gift), so I don't expect some sort of vast improvement but it used to run MUCH smoother and quicker and I don't want to see it die on me!

Thanks so much guys. I think the MalWareBytes download may have done the trick, as I have just restarted my computer after a full scan to see that my CPU and RAM gauges are much lower as well as noticing what seems to be a much faster system overall.

Reading about Alureon, is there anything I need to do aside from changing passwords on certain websites that have some of my confidential information?

Oh, and Layback - I also ran the Kaspersky root/bootkit tool and it found and removed something so it looks like it's smooth sailing!