Context : Disclosing the structure of disks surrounding Herbig AeBe stars is important to expand our understanding of the formation and early evolution of stars and planets . The first astronomical units of these disks in particular , because they are hot , dense , and subject to intense radiation field , hold critical clues to accretion and ejection processes , as well as planet formation in environment different than what prevailed around our own early Sun . Aims : We aim at revealing the sub-AU disk structure around the 10 Myr old Herbig Be star HD 100546 and at investigating the origin of its near and mid-infrared excess . Methods : We used new AMBER/VLTI observations to resolve the K-band emission and to constrain the location and composition of the hot dust in the innermost circumstellar disk . Combining AMBER observations with photometric and MIDI/VLTI measurements from the litterature , we revisit the disk geometry using a passive disk model based on 3D Monte-Carlo radiative transfer ( including full anisotropic scattering ) . Results : We propose a model that includes a tenuous inner disk made of micron-sized dust grains , a gap , and a massive optically thick outer disk , that successfully reproduces the interferometric data and the SED . We locate the bulk of the K-band emission at \sim 0.26 AU . Assuming that this emission originates from silicate dust grains at their sublimation temperature of 1500 K , we show that micron-sized grains are required to enable the dust to survive at such a close distance from the star . As a consequence , in our best model , more than 40 % of the K-band flux is related to scattering , showing that the direct thermal emission of hot dust is not always sufficient to explain the near-infrared excess . In the massive outer disk , large grains in the mid-plane are responsible for the mm emission while a surface layer of small grains allows the mid and far infrared excesses to be reproduced . Such vertical structure may be an evidence for sedimentation . The interferometric observations are consistent with a disk model that includes a gap until \sim 13 AU from the star and a total dust mass of \sim 0.008 lunar mass ( \sim 6.10 ^ { 23 } g ) inside it . These values together with the derived scale height ( \sim 2.5 AU ) and temperature ( \sim 220 K ) at the inner edge of the outer disk ( r = 13 AU ) , are consistent with recent CO observations . Conclusions :