I know I have a virus but my virus protection does not detect.

[ELProdigy]

I downloaded something that essentially gave me a Trojan virus. I immediately preformed a full scan on malware bytes and delete the the virus. Well now I see add popups in some websites and the proxy settings got messed up as well. Some of the applications such as Desura will not let me login because of the proxy. I have downloaded an adware remover but it says that my pc is clean. How can I fix this. Also my friend suggested bombing it and erasing the pc to its factory settings but I don't know if that will work.

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