Terahertz (THZ) band stop filter can be used to filter interference signals in a filter pass band. The quality factor (Q) is the most important index to evaluate the transmission performance of filter. Usually, the high Q, the narrow bandwidth and the large slope of the stop band will promise the good filtering accuracy and transmission response. However, the Q value taken from metamaterial structures designed on the plane is always only in the single digit, resulting in less than satisfactory in filtering performance. Herein, a high Q terahertz band stop filter based on metamaterials was proposed. To fabricate this three-dimensional (3D) metamaterial structure, a microtopographic substrate guided method with feasible and high accuracy capacities was proposed. As a result, the device is measured to be in the filtering state in 1.038-1.102 THz while it is stopped in 1.062-1.066 THz. The similarity between the experimental and simulated transmission is up to 86.32%, indicating the fabricating method possesses a high accuracy. Accordingly, the Q value was calculated to be as high as 532. The band stop filter with this record Q value can be widely used in THZ detection, imaging and sensing in future. Meanwhile, the proposed fabrication method is effectively applied in 3D metamaterial and THZ device as well.