Windows 7 Stops Start up and comand prompt window

I was recently hit by a bad virus and was able to remove however without some damage to my system. It is a Lenova ThinkPad laptop. When my Windows 7 boots up to the sign in window, I am able to log in, the system starts up but stops at a command prompt window. I have to type in "explorer" then Windows starts, I close command window and all works fine. I do not have access to my original...