A trojan has altered my internet connection

My visiting nephew managed to get a trojan on my pc that disrupted my internet explorer from working, but aol managed to stay online. When I tried to completely reset the pc with a reboot the Trojan had managed to block ALL online activity, completely shutting me offline. When I talked to a service rep on the phone (hung up before I got charged 149$) he told me the Trojan had altered my internet connection and I had to somehow restore it or fix it. Anyone know how to do this?

Update: The rest of the system seems fine, I was using spyware doctor and AVG my computers operating systems is an

AMD athlon(TM) 64x2 Dual core processor 5,000+
2.64ghz. 2 gigs of ram

my friend online told me to create a "killdisk" which I did in order to destroy everything and then reboot pc with disk but; somehow I didn't do it right, a solution to using the killdisk properly or fixing the pc in a less violent method would be great