Theoretical analysis can impart great benefits on the rationale design of 3D photonic structures by revealing the underlying mechanisms of structural distortion during each processing step. In this report, we quantitatively study the distortion of a three-term diamond-like structure fabricated in SU-8 polymer by four-beam interference lithography, which can be attributed to refraction at the air-film interface, and resist film shrinkage during lithographic process. In study of photonic bandgap (PBG) properties of Si photonic crystals templated by the SU-8 structures, we find that the distortion has degraded the quality of PBGs. Furthermore, we theoretically design new optical setups to fabricate three-term diamond-like structure with minimal deformation. Instead of single exposure of four beams, we use triple exposure of two beams, one from the central beam and the other from the side beam each time. A set of new linear polarization vectors is suggested to enhance the contrast between the minimal and maximal intensities of interference pattern.