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Digital holographic microscopy allows measuring the complex wavefront reflected by or transmitted through a sample from a single hologram acquisition. In reflection configuration, assuming an homogeneous surface composed of a unique material, and excluding multiple reflections from underlying layers, the topography of the surface is proportional to the reconstructed phase and the topography can be retrieved with a so-called interferometric resolution. But, in presence of semi-transparent multilayers, the topography is no longer proportional to the reconstructed phase: multiple reflections from and between the layers interfaces modify the reflected wavefront. In this paper we demonstrate that using the complex wavefront information, i.e. not only the phase, acquired at several discrete wavelengths, we retrieve the topography by comparing the measured wavefront with the theoretical reflected wavefronts calculated from the model of the multilayers structure. The principle is demonstrated by comparing DHM and mechanical profilometer measurements for: staircase SiO2 on a Silicon substrate, hole dug by SIMS (Secondary Ion Mass Spectrometry) in a transparent multilayer films, and fluid (Tetraethylene-glycol) on a Si substrate.