In single patterning, the increase of odd order diffractive power and decrease of even order diffractive power may improve the wafer alignment performance. A Fourier model is given to quantitatively describe the diffractive optical power of grating structures. Four novel alignment mark structures with higher odd order wafer qualities (WQs) have been optimized based on the model. The accuracy of our model has been validated with almost the same results for different alignment marks using our model and rigorous coupled wave analysis (RCWA). Moreover, three dimensions (3D) of alignment mark should be optimized to get higher WQs for self-aligned double patterning (SADP). Our paper proposes a model to simplify the 3D RCWA algorithm where WQs of SADP grating structures could be split into two different one-direction grating structures. The advantage of the equation makes the evaluation of different grating period of SADP mark fast, accurate and simple. The models and structures of all the designed alignment marks will make it easier for engineers to choose the property alignment mark faced with single patterning or SADP process.