Digital holographic microscopy (DHM) is an interferometric technique that allows real-time imaging of the entire complex optical wavefront (amplitude and phase) reflected by or transmitted through a sample. To our knowledge, only the quantitative phase is exploited to measure topography, assuming homogeneous material sample and a single reflection on the surface of the sample. In this paper, dual-wavelength DHM measurements are interpreted using a model of reflected wave propagation through a three-interfaces specimen (2 layers deposited on a semi-infinite layer), to measure simultaneously topography, layer thicknesses and refractive indices of micro-structures. We demonstrate this DHM reflectometry technique by comparing DHM and profilometer measurement of home-made SiO(2)/Si targets and Secondary Ion Mass Spectrometry (SIMS) sputter craters on specimen including different multiple layers.