AbstractPhotonic integrated circuits (PICs) are iterating on electronic ones to enable higher‐speed parallel computing while meeting the growing demands for energy efficiency in big‐data processing. However, manufacturing multi‐layered and 3D PICs remains challenging based on conventional planar lithography. Here, a rapid prototyping technique is delineated to configure large‐area and 3D PIC in glass based on laser‐direct written optical waveguides by employing femtosecond cylindrically polarized vortex laser beams. The vortex laser beam is mathematically rotationally invariant and capable of conformally transforming waveguide cross‐sections at arbitrary bending angles of 0–90° and across a large depth change. Based on this approach, a one‐layer 12‐core waveguide circuit with a variable cross‐section (diameter 5–11.5 µm) while maintaining a high mode ellipticity >0.974, as well as a more complex three‐layer 36‐core connector in which the waveguide dives continuously from 50 µm to 550 µm with a small loss difference of <0.1 dB is demonstrated. This work offers a pathway for 3D imprinting of large‐area photonic circuits in glass and other transparent materials, which has potential applications in high‐efficiency photonic computing, multidimensional quantum networks, and 3D optics topology.