Fastener assembly is a tedious and time-consuming work because operators have to check assembly manuals and find right fastener for each hole. Hence, this paper aims to develop a three-dimensional (3-D) projection system that projects assembly instruction onto the work piece surface directly to guide operators to assemble. However, in order to project the instruction accurately, the corresponding part of the computer-aided design model of the physical scanned area needs to be attained through the rapid and accurate registration. In order to achieve this goal, first, a high-accuracy and rapid 3-D measurement system is developed; second, a fast registration method based on local multiscale geometric feature vector is proposed to accelerate the registration speed and improve the registration reliability. Experimental results demonstrate the measurement accuracy of the developed system, and verify the feasibility of the proposed registration method. Hence, the proposed method can lead to improved assembly efficiency and decreased error probability, making great contributions to large-scale structure assembly.