A three-dimensional micro-channel structure includes a plurality of layers arranged in a stack, each layer having one or more separate micro-channels having first, second, and third ports spatially aligned in the stack so that the first, second, or third ports each form one or more first, second, or third contiguous areas, respectively, that do not include other ports. Each of the contiguous areas includes at least one port from each of two or more layers in the stack. One or more pipes having an open side each covers only one contiguous area.