An image data area extracting system includes: a threshold value setting unit configured to set a threshold value for three dimensional image data of an object; an area managing unit configured to extract a threshold value area from the three dimensional image data based at least in part on the threshold value; a three dimensional projection image display unit configured to display an image, the image being constructed from the three dimensional image data; a starting point designating unit configured to designate a starting point for a connected area to be deleted from the image; and an extract connected area deleting unit configured to remove the connected area from the image.