This work aims at a quantitative simulation of instrumented indentation test based on physics of crystal plasticity. Indentation loading is associated with a complex 3D deformation path: it can be viewed as an ideal benchmark to test various crystal plasticity assumptions. For large scale indentation (micron size), a 3D numerical simulation using finite element crystal plasticity (FEM) is setup and quantitatively compared to experimental results using critical constraints: the load/stiffness-displacement curves and the surface displacements. Various set of parameters obtained from Dislocation Dynamics (DD) are used. A comparison with experiments shows the dominant effect of initial dislocation density and slip system interactions. For smaller depth (maximum 100 nm), Dislocation Dynamics coupled simulations to FEM are setup. Since this approach does not provide defect nucleation rules, several strategies are implemented and tested: fitting to Molecular Dynamics (MD) load-depth curve for spherical tip, or automatic generation of deformation accommodating dislocation (GND) for conical tip geometry for example. In this framework, size effects show up in the modification of the dislocation structures with depth through critical expansion of dislocation loops and junction formation.