Fast tool servo diamond turning is a promising machining method for precision and complex micro-structured surfaces with spatial wavelength above tens of microns. It is crucial to measure and characterize the micro-structured surfaces to sub-micrometer form accuracy. The general purpose measurement instruments are not able to evaluate the true form accuracy between the measured surface and designed surface. Therefore, in this paper an automatic surface characterization method is proposed to evaluate the form accuracy for micro-structured surfaces. The fabricated surfaces can be measured by any high-resolution measurement instruments. After the surface measurement, an iterative closest point (ICP) algorithm is modified to align the measured surfaces to the designed surfaces with the form error evenly distributed over the whole surface. After alignment, the designed surface height corresponding to each measured point is calculated to form the areal error map. 3D surface parameters are chosen and calculated from the error map to characterize the surface form error. Experimental results demonstrate the effectiveness of the proposed surface characterization method.