Method of manufacturing a microelectronic device

Method of manufacturing a microelectronic device, for example a photonic device, particularly a photodiode, comprising the following steps:

• a) providing a substrate comprising a cavity formed from a first main surface of the substrate, a bottom of the cavity being made of a first material, the first main surface of the substrate being made of a second material,
• b) performing a selective epitaxy of a third material in the cavity of the substrate, until the epitaxial material fills the cavity and protrudes out of the cavity by a so-called protrusion thickness, whereby an epitaxial structure is obtained,
• c) depositing an encapsulation layer made of a fourth material on the substrate and on the epitaxial structure,
• d) carrying out a CMP thinning step to remove the encapsulation layer and the portion of the epitaxial structure protruding from the first main surface of the substrate, the thickness of the deposited encapsulation layer being in the range from 20 to 200% of the protrusion thickness.