Micro-manufacturing with a Two-Photon Polymerization (TPP) technique is an emerging manufacturing technique to produce small objects of tens of μm size. Combined with three axes numerically controlled equipment, it becomes possible to produce a wide diversity of product shapes. As a result, controlling this equipment while taking into account the manufacturing constraints raises the problem of trajectory generation. It is the purpose of this paper to show how this trajectory generation process can take advantage of the three numerically controlled axes to produce complex-shaped objects. Here, it is shown how the concept of layered manufacturing commonly used in rapid prototyping can be superseded by a combination of different path planning strategies, much in the same way free-form surfaces or complex shapes can be produced with classical milling machines. Through the proposed process, the boundary decomposition process applied to an object reduces to a set of sub-domains where groups of parallel trajectories are generated. The proposed trajectory generation process takes also into account the manufacturing constraints specific to TPP to produce microstructures of high quality. Examples of products illustrate the proposed approach and demonstrate its capabilities.