Is there any way to remove the windows security alerts from the windows taskbar, as they are really annoying, especially when you are trying to remove something, and it just keeps popping up over and over again that your system is infected.

is the windows firewall disabled?
if not then try it, although im not sure it will get rid of it

All of the default windows protection is disabled, I only ever use software like McAfee for firewalls, I don't like Microsofts software.

Disable the windows security center alerts by going to start > control panel > Security center > then the box down at the left hand corner  "Change the way security center alerts me" and untick the boxes. 

hmm well i look at an article which i found on google. you basically need to tell windows that your are protected
heres the link
http://www.askdavetaylor.com/how_do_i_get_rid_of_...curity_alerts.html

[Edit] lol Chr1s' way works too

I completely forgot about this thread until now, thanks a lot.