A new experimental method aiming to the characterization of self-affine rough surfaces is presented. Based on a three dimensional reconstruction of the relief from stereo pairs obtained with a scanning electron microscope, it allows a non-destructive quantitative analysis of fracture surfaces, with a xy and z resolution only slightly lower than the original images. The roughness index of the fracture surface of an aluminum alloy is recovered, as well as the Hurst exponents of reconstructed computer-generated fractional Brownian reliefs.