With excellent mechanical and optical properties, sapphire substrate becomes a very important industrial material especially for LED manufacturing. Its quality control requires two tasks, double-sided surface profiling and defect detection. In this paper, a 3D surface scanning system is proposed as a platform for sapphire substrate inspection. During the scanning process, the height information of both upper and lower surfaces is measured by a chromatic confocal probe. For lateral positioning feedback, an in-house developed sensor, namely, image grating, is introduced in this paper. For these inspection processes, there are three challenges: 1) the motion error in the vertical direction, 2) simultaneous measurement of both upper and lower surfaces, and 3) lateral positioning error in a large scanning area. To address these challenges, three key technologies were developed: 1) real-time motion error compensation based on a fringe interferometer, 2) a double-sided measurement for transparent specimen without the pre-knowledge of its refractive index, and 3) planar image grating pair for accurate 2D displacement feedback. The experimental results showed that the proposed measurement system was able to achieve 50 nm accuracy of the standard deviation when measuring the step height of gauge blocks. When the system measured 4-inch double-sided polished sapphire substrate, the measurement repeatability of TTV (Total Thickness Variation) was within 60 nm; and that of warpage was within 10 nm. As a side product, refractive index can also be measured using the proposed system, and experimental results showed respectable consistency. •A motion error compensation system is proposed based on film interferometry.•By setting up a pair of image gratings, lateral positioning errors and 2D Abbe error can be minimised.•The proposed technology is able to achieve nanometer repeatability in measuring thickness variation and warpage.•This system is able to simultaneously measure transparent specimens without having to know the refractive index.•The proposed system can also be used for general surface topography measurement purposes.