1. A 3D profiling system of a semiconductor chip comprising: 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 the SEM images; an extraction unit that performs principal component analysis (PCA) on the gray levels of the SEM images and separates principal components among the plurality of different components; and a calculation unit that receives 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.