Fighting system Viruses the hard way…..

I have been trying to understand viruses and fight them by trying to trace them down in the system usibg programs like Adaware or Spybot to find them for me. I know i got to kill it in the RAM as well as on the HD…But my issue is that I kill the process running it and delete the file and empty the trash bin and the virus is is still there….I know AV can destoy them but how can we root them out manually and kill them?