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A procedure to generate a suitable surface and volume meshes from image sequences or other scan data is presented. The methodology gives preference to readily available free software for the final goal of using the generated mesh for computational fluid dynamics or finite element simulations. The steps involve the extraction of a surface mesh from the image sequence, segmentation, trouble-shooting, treatment, refinement/coarsening, smoothing, translation into a volume mesh and post-processing. The user controls the detail of the final mesh through a series of algorithms included in the suggested software. The methodology is illustrated with a computer microtomography data of a carbonate rock. Finally, the mesh is imported in ANSYS® Fluent to demonstrate that the resulting mesh can be used in simulations.