A multi-layer fabrication method for making three-dimensional structures is provided. In one embodiment, the formation of a multi-layer three-dimensional structure comprises: 1) fabricating a plurality of layers with each layer comprising at least two materials; 2) aligning the layers; 3) attaching the layers together to form a multi-layer structure; and 4) removing at least a portion of at least one of the materials from the multi-layer structure. Fabrication methods for making the required layers are also disclosed. In another embodiment, the formation of a multi-layer three-dimensional structure comprises: 1) attaching a layer of a material to a substrate or a previously formed layer; 2) machining the attached layer to form a layer that comprises at least two materials; and 3) repeating the operations of 1) and 2) a plurality of times to form a multi-layer structure; and 4) removing at least a portion of at least one of the materials from the multi-layer structure to form a desired three-dimensional structure.