For an optimization of a drilling process to minimize burr formation, control chart or empirical model from design of experiment can be used. However, direct measurement of inter-layer burr is limited experimentally in the case of drilling through a multi-layered material, which is a common process in aerospace industry. A finite element model that can quantitatively predict the inter-layer burr formation from workpiece material properties and process conditions would significantly reduce the cost and time for building an empirical model. In this study, a finite element model using material properties of stainless steel 304L from previous work was applied to simulated burr formation process during drilling of a multi-layered material. Simulation showed inter-layer burr formation along with entrance burr formation. A quantitative prediction scheme of burr size using node displacement tracking for burr thickness and height was presented.