Bluetooth Low Energy (BLE) based localization is a next candidate for indoor localization. In this paper, we propose a new BLE-based fingerprinting localization scheme that improves localization accuracy. BLE is a narrow bandwidth communication that is highly affected by frequency selective fading. Frequency selective fading is mainly caused by multipaths between a transmitter and receiver, which are dependent on channels. We utilize channel specific features by separately measure received signal strength (RSS) on different channels to improve localization accuracy. BLE standards provide no API to retrieve channel information of incoming packets. We therefore developed a separate channel advertising scheme to separately measure RSS on different channels. To demonstrate the feasibility of the separate channel fingerprinting, we conducted preliminary experiments as well as initial evaluations. Experimental evaluations demonstrated that the separate channel fingerprinting improves localization accuracy by approximately 12%.