A three-dimensional numerical method for the prediction of transient temperatures reached during realistic braking operations in a ventilated disk brake assembly is presented in this paper. This Layered FFT-FEM numerical method (Fast Fourier Transform-Finite Element Method) takes advantage of the high Peclet number “skin effect” to decouple the moving boundary contact problem from the spatially periodic but non-axisymmetric cooling associated with the vents. The first problem is modeled according to the FFT-FEM method developed previously by the authors. This technique succeeded in using high Peclet numbers for axisymmetric moving solids submitted to general loading conditions. No numerical convergence problems are encountered and short computer time is required. The second problem is modeled according to traditional three-dimensional finite element techniques. The Layered FFT-FEM results are compared with analytical results. A braking operation is simulated for an industrial ventilated disk brake.