With the increasing sophistication required in integrated-optical devices it has become necessary to develop accurate methods that allow for an optimization of component design. In this paper we present an overview of the theory and the experimental conditions needed to obtain optical cross sections applicable to rare-earth doped materials. The values generated by the method provide the accuracy needed in the modelling of rare earth-doped integrated devices. As a test case, we have applied the method to the 4I13/2 → 4I15/2 transition of Er3+-doped LiNbO3 crystals and Zn diffused Er:LiNbO3 channel waveguides developed in our laboratory. Adverse effects of concentration determination and ion-clustering are investigated.