Flow diverter stents are now increasingly utilised in the management of cerebral aneurysms. Computed flow simulation can be used to assess flow reduction and anticipate treatment outcome. To achieve this, the stent must be deployed virtually in the parent vessel carrying the aneurysm before running the simulation. This study proposes an alternative method to virtual deployment using micro-computer tomography after in vitro deployment of stents in silicone models to reconstruct accurately the struts over the aneurysm neck. Two experienced neuroradiologists deployed different stents (four 48-wire and one 64-wire pipeline embolization devices) in identical silicone models. Micro-CT acquisition was then carried out and allowed to reconstruct the stent meshes very accurately using different pre-processing steps. Virtual deployments were also performed for the two types of stents. Qualitatively, it was shown that the real deployments formed an inhomogeneous wire network compared to the regularity of the mesh of the virtually deployed stents. This difference had a moderate influence on hemodynamics. For virtual deployment, we observed an overestimation of the flow reduction of 5% and 16% for the 64- and 48-wire stents, respectively. While the flow patterns remained the same for the 48-wire stent, the 64-wire stent showed an inversion of the intra-aneurysmal vortex. This promising method could be used in the development of flow diverter devices or to conduct a comparative evaluation between different devices.