Making Use of Arduino Bootloader but no arduino libraries in Atmel Studio

Hello, I would like to use Arduino Uno with Atmel Studio 6.2. But I would like to use only the boot loader available in Arduino and use my custom code. So the bootloader is used only to load my custom code through USB which does not use any Arduino libraries. How should I configure the Atmel Studio? What is the External programmer I need to configure to make use of this USB boot loader?