In this study, three-dimensional (3D) polyacrylamide microstructures containing gold nanorods (AuNRs) were fabricated by two-photon polymerization (TPP) using Rose Bengal (RB) as the photoinitiator. To retain AuNRs in the 3D polymer microstructures, the laser wavelength was chosen for two-photon RB absorption for improved TPP efficiency, but not for enhancing the longitudinal plasmon resonance of AuNRs which may result in photothermal damage of AuNRs. After TPP processing, the laser wavelength was tuned for the longitudinal plasmon resonance and the laser power was increased to beyond the damage threshold of the AuNRs for reshaping the AuNRs into gold nanospheres. As a result, AuNRs in designated positions of the fabricated 3D microstructures can be achieved. Two-photon luminescence from the doped AuNRs can also act as contrast agent for the visualization of 3D polymer microstructures.