Aspects of the present disclosure relate generally to preparing models of three-dimensional structures. In particular, a model of a three-dimensional structure constructed of porous geometries is prepared. A component file including a porous CAD volume having a predefined portion of a boundary. A space including the porous CAD volume is populated with unit cells overlapping the predefined portion of the boundary. The unit cells are populated with porous geometries having a plurality of struts having nodes on each end. At least a first strut overlaps the predefined portion of the boundary and has a length, a first node outside the porous CAD volume, and a second node inside the porous CAD volume. All struts entirely outside the porous CAD volume are removed. After removal of the struts entirely outside the porous CAD volume, each of the remaining struts is connected to a node at each end thereof.