Morphogenesis is a general concept in biology including all the processes which generate tissue shapes and cellular organizations in a living organism. Many hybrid formalizations (i.e., with both discrete and continuous parts) have been proposed for modelling morphogenesis in embryonic or adult animals, like gastrulation and wound healing. We propose first to study the ventral furrow invagination as the initial step of gastrulation, early stage of embryogenesis. We focus on the study of the connection between the apical constriction of the ventral cells and the initiation of the invagination. For that, we have created a 3D biomechanical model of the embryo of the Drosophila melanogaster based on the Finite Element Method. Each cell is modelled by an elastic hexahedron contour and is firmly attached to its neighbouring cells. A uniform initial distribution of elastic and contractile forces is applied to cells along the model. Numerical simulations show that invagination starts at ventral curved extremities of the embryo and then propagates to the ventral medial layer. Then, this experimental observation can be attributed uniquely to the specific shape of the embryo and we provide mechanical evidence to support it. Results of the simulations of the “pill-shaped” geometry of the Drosophila melanogaster embryo are compared with those of a spherical geometry corresponding to the Xenopus lævis embryo. Eventually, we propose to study the influence of cell proliferation on the end of the process of invagination represented by the closure of the ventral furrow and compare final embryo’s shapes with and without proliferation.