A 3D profiling system of a semiconductor chip is provided and includes a storage unit that receives scanning electron microscope (SEM) images of a plurality of semiconductor devices having respective data with respect to a plurality of different components and gray levels of each SEM image. An extraction unit that performs principal component analysis (PCA) on the gray level of the SEM image and separates principal components from among the plurality of different components is also part of the system. Additionally, a calculation unit receives provision of actually measured values of the plurality of semiconductor devices, and applies a multiple linear regression to the principal components based on the measured values to complete a 3D profile of the semiconductor chip.