Outside surface fluctuations of inertial confinement fusion (ICF) capsule greatly affect the implosion performance. An atomic force microscope (AFM)-based profilometer is developed to precisely characterize the capsule surface with nanometer resolution. With the standard nine surface profiles and the complete coverage data, 1D and 2D power spectra are obtained to quantitatively qualify the capsule. Capsule center fast aligning, orbit traces automatic recording, 3D capsule orientation have been studied to improve the accuracy and efficiency of the profilometer.