Atmel Studio comes with a command line utility called atprogram that can be used to program targets using the Atmel AVRISP mkII. During the Atmel Studio installation a shortcut called Atmel Studio 7.0 Command Prompt were created in the Atmel folder on the Start menu. By double clicking this shortcut a command prompt will be opened and programming commands can be entered. The command line utility is installed in the Atmel Studio installation path in the folder Atmel/Atmel Studio 7.0/atbackend/.
atprogram --help