Abstract Femtosecond laser ablation of materials is turning to be an important tool for micromachining as well as for selective removal of biological tissues. In a great number of applications, laser ablation has to process through interfaces separating media of different properties. The investigation of the ablation behavior within materials and passing through interfaces is the main aim of this study. Especially, the analysis of the discontinuity in the ablation profile close to interfaces between distinct materials can reveal some of the phenomena involved in the formation of an ablated microcavity geometry. We have used a method that correlates the ablation cross sectional area with the local laser intensity. The effective intensity ablation properties were obtained from surface ablation data of distinct materials. The application of this method allows the prediction of the occurrence of a size discontinuity in the ablation geometry at the interface of distinct media, a fact which becomes important when planning applications in different media.