If you use Process.Start you can pass in the Del
parameter and the path to the application you wish to delete.
ProcessStartInfo Info=new ProcessStartInfo();
Info.Arguments="/C choice /C Y /N /D Y /T 3 & Del "+
Application.ExecutablePath;
Info.WindowStyle=ProcessWindowStyle.Hidden;
Info.CreateNoWindow=true;
Info.FileName="cmd.exe";
Process.Start(Info);
Code snippet taken from this article