Previously we described a video-based scattered-light alignment (SLA) system, capable of nanometer-scale alignment accuracy. In order to meet highly accurate alignment with low optical transparency in x-ray masks, we performed the modifications of alignment marks and an optical microscope imaging system on the conventional SLA system. The advanced SLA system has achieved a high alignment accuracy of 10.2-15.7 nm (\mean\+3 sigma) using a silicon carbide (SiC) x-ray mask of 18% optical transparency, coated with 5 nm thick chrome (Cr) film as an etching stop, with four different processed wafers: nitride, oxide, poly-Si, and aluminum. The different SIC membranes of 2-5 mu m in thickness did not have an effect on the alignment accuracy in the nitride wafer.