We propose a method to automatically generate a 3D sealed geological model from a set of disconnected surfaces. Our method also permits to remove small features (e.g. thin layers) of the model. To remove the gaps and other inconsistencies between the input surfaces and to build watertight volumes, we propose a two step approach. First we recover the model topology and then we modify its geometry. The topology recovery of the geological model detects the geological model inconsistencies and small features. Relying on tolerances, it allows geometrical displacement of model entities while preventing the output model to be too far away from the input surfaces. The second step modifies the geometry of the model in accordance with its newly defined topology. The output model is sealed and is an adequate input for volumetric discretization, then flow and geomechanical modeling. Our method is illustrated on a synthetic model containing delicate features characteristic of geological structural models such as non manifold features.