Objectives: We are interested in the numerical simulation of the anastomotic region comprised between outflow canula of LVAD and the aorta. Segmentation, geometry reconstruction and grid generation from patient specific data remain an issue because of the variable quality of DICOM images, in particular CT-scan (e.g. metallic noise of the device, non-aortic contrast phase). We propose a general framework to overcome this problem and create suitable grids for numerical simulations. Methods: Preliminary treatment of images is performed by reducing the level window and enhancing the contrast of the greyscale image using contrast limited adaptive histogram equalization. A gradient anisotropic diffusion filter is applied to reduce the noise. Then, watershed segmentation algorithms and mathematical morphology filters allow reconstructing the patient geometry. This is done using the InsightToolKit library (www.itk.org). Finally the Vascular Modeling ToolKit (www.vmtk.org) and gmsh (www.geuz.org/gmsh) are used to create the meshes for the fluid (blood) and structure (arterial wall, outflow canula) and to a priori identify the boundary layers. The method is tested on five different patients with left ventricular assistance and who underwent a CT-scan exam. Results: This method produced good results in four patients. The anastomosis area is recovered and the generated grids are suitable for numerical simulations. In one patient the method failed to produce a good segmentation because of the small dimension of the aortic arch with respect to the image resolution. Conclusions: The described framework allows the use of data that could not be otherwise segmented by standard automatic segmentation tools. In particular the computational grids that have been generated are suitable for simulations that take into account fluid-structure interactions. Finally the presented method features a good reproducibility and fast application.