3-D profiles of discontinuous surfaces patterned with high step structures are measured using four wavelengths generated by phase-locking to the frequency comb of an Er-doped fiber femtosecond laser stabilized to the Rb atomic clock. This frequency-comb-referenced method of multi-wavelength interferometry permits extending the phase non-ambiguity range by a factor of 64,500 while maintaining the sub-wavelength measurement precision of single-wavelength interferometry. Experimental results show a repeatability of 3.13 nm (one-sigma) in measuring step heights of 1800, 500, and 70 μm. The proposed method is accurate enough for the standard calibration of gauge blocks and also fast to be suited for the industrial inspection of microelectronics products.