This article presents a layered decomposition method to decompose the machined surface into sub-surfaces with different components in dissimilar scale to identify machining errors. The high-definition metrology-measured data of the surface is first fitted by triangular mesh interpolation method to separate the surface into two sub-surface components, namely, system error caused and random error caused, respectively, whereas the stability of sub-surface entropy is used as the criteria to determine the refined mesh in case the decomposition exists throughout. Then, the sub-surface of system error is further decomposed by bi-dimensional empirical mode decomposition to get the error components varying in scales: surface roughness, waviness and profile, and as a result to identify the machining errors. Finally, self-correlation analysis is applied to each component to verify the decomposition. The result shows that each decomposed component has a distinctive wavelength, which proves that the method can successfully decompose the comprehensive surface topography into different scale components.