My system is infected by spyware that keeps popping up on the screen . What to do?

Hello! I did the whole process described on Spybot S&D, and now Spybot shows that no more spywares present in my system. However, when I scan my computer with Spyware Doctor it shows around 4 threats and 31 infections tainting my system. Besides, one of those programs keeps popping up saying "system security warning" (a spyware). What should I do? Please help!