We present a mechanism to efficiently pre-select the number of intrinsic many-body states that are used to define the many-body wave functions within the discrete Generator Coordinate Method (GCM). This procedure, based on the proper definition of a natural basis of orthonormal states, does not require the evaluation of the non-diagonal Hamiltonian kernels to do the selection and helps to reduce the numerical instabilities. The performance of the method is analyzed in detail in the ground state and 0⁺ excited states of some selected nuclei computed with the Gogny energy density functional.