Objective The identification of lower limb axes plays an important role in the kinematics research and clinical operation of total knee replacement surgery. This paper presents a method to extract the femoral axes based on CT images automatically. Method Using a series of image pre-processing algorithms such as segmentation, smoothing and rotations of the images, to get the 3-D fine mesh of lower limb bones. Then, by analyzing the morphological feature of 3-D femoral surface and based on the definitions of femoral mechanic axis and femoral anatomical axis, three feature points located on femoral head, femoral distal intercondylar notch and femoral shaft centre are selected to define the mechanical and anatomical axes of femur. In the light of the morphological feature of femur head, the center of femoral head was decided according to the changes of the gradient between each cross section of the femoral head. Meanwhile, we got the center of femoral intercondylar notch by calculating the closed-loop zone of cross sections of the bone. Those two points could finally define the mechanical axis of the femur. Result Based on a series of image processing procedures, three dimensional (3-D) surface model of lower limb bone were generated. By analyzing the morphological features of femoral head and knee joint center, a simple and convenient way was proposed to extract the coordinate of three feature points and further the femoral axes automatically. Conclusions Experimental results show that this processing procedure can extract the femoral mechanic axis and femoral anatomical axis precisely with 3-D CT images.