The shape‐shifting behavior of liquid crystal networks (LCNs) and elastomers (LCEs) is a result of an interplay between their initial geometrical shape and their molecular alignment. For years, reliance on either one‐step in situ or two‐step film processing techniques has limited the shape‐change transformations from 2D to 3D geometries. The combination of various fabrication techniques, alignment methods, and chemical formulations developed in recent years has introduced new opportunities to achieve 3D‐to‐3D shape‐transformations in large scales, albeit the precise control of local molecular alignment in microscale 3D constructs remains a challenge. Here, the voxel‐by‐voxel encoding of nematic alignment in 3D microstructures of LCNs produced by two‐photon polymerization using high‐resolution topographical features is demonstrated. 3D LCN microstructures (suspended films, coils, and rings) with designable 2D and 3D director fields with a resolution of 5 µm are achieved. Different shape transformations of LCN microstructures with the same geometry but dissimilar molecular alignments upon actuation are elicited. This strategy offers higher freedom in the shape‐change programming of 3D LCN microstructures and expands their applicability in emerging technologies, such as small‐scale soft robots and devices and responsive surfaces.