Single-lens-based optical range finding systems were developed as an efficient, compact alternative for conventional stereo camera systems. Among various single-lens-based approaches, a multiple color-filtered aperture (MCA) system can generate disparity information among color channels, as well as normal color information. In this paper, we consider a dual color-filtered aperture (DCA) system as the most minimal version of the MCA system and present a novel inter-color image registration algorithm for disparity estimation. This proposed registration algorithm consists of three steps: (i) color channel independent feature extraction; (ii) feature-based adaptive weight disparity estimation; and (iii) color mapping matrix (CMM)-based cross-channel image registration. Experimental results show that the proposed method can not only generate an accurate disparity map, but also realize high quality cross-channel registration with a disparity prior for DCA-based range finding and color image enhancement.