Femtosecond laser surface processing (FLSP) is a material processing technique used to produce self-organized micro/nanostructures on metals. The hierarchal structures can improve the surface properties of materials when applied to specific applications such as enhancing heat transfer. In this paper, we demonstrate a recently developed technique termed multi-material, multi-layer FLSP (3ML-FLSP). With 3ML-FLSP, micro/nanoscale features can be produced that are composed of multiple materials by processing surfaces using traditional FLSP techniques that are layered with thin foils of different materials. We demonstrate results with three layers of different metals (304 stainless steel, copper, and aluminum) clamped together during laser processing to create structures composed of all three metals. Ion beam milling is used to cross-section structures for subsurface analysis of the microstructure. The three metals did not mix within the bulk of the microstructures indicating that the microstructures were produced primarily through preferential removal of material around the structures. However, there was mixing of all three materials within the nanoparticle layer that covers the microstructures.