A method, and a system for implementing the method, are disclosed wherein coordinates of survey region are used to locate small pieces of a seismic wave model, usually defined by their nodes (or vertices) and contain information about physical properties, such as liquid or solid, density, velocity that seismic waves propagates in it; and connects them to the appropriate source and receiver sensor. In particular, the method and system disclosed, generates a multi-layer mapping of the survey region by decomposing the survey region into cubes containing small pieces of seismic wave models (the elements), as well as source and receiver location. Those cubes are then indexed depending upon their location and the elements, sources and receivers are assigned to a particular cube thereby creating a multi-layer relationship between the survey region map, the cube map, the elements map, as well as the source and receiver locations.