Accurate measurement of lower limb alignment is vital for orthopedic surgery planning. Based on the 3D lower limb bone models reconstructed from CT images, a 3D feature construction system is developed to find the lower limb alignment. This paper presents new methods to automatically identify the anatomic axes, mechanical axes, joint center points, and reference planes of the lower extremities. As far as we know, there is no other system that can construct all these features automatically. With the above identified features, our system can calculate the related angles of the lower limb alignment accurately for orthopedic knee surgery planning. We applied our system on two groups of specimen (with 6 pairs of lower limbs), and the resulting related angles are identical to the actual angles of the lower limb alignment.