The quantification problem of recovering the original material distribution from secondary ion mass spectrometry (SIMS) data is considered in this paper. It is an inverse problem, is ill-posed and hence it requires a special technique for its solution. The quantification problem is essentially an inverse diffusion or (classically) a backward heat conduction problem. In this paper an operator-splitting method (that is proposed in a previous paper by the first author for the solution of inverse diffusion problems) is developed for the solution of the problem of recovering the original structure from the SIMS data. A detailed development of the quantification method is given and it is applied to typical data to demonstrate its effectiveness.