The word gem refers to any precious or semi precious stone. Anatomy is a branch of art and history, comprising the study of identification, description and interpretation of the content of images.
It also includes the subjects depicted, the particular compositions and details used to implement the same. Apart from that, it also talks about other elements that are distinct from artistic style in 2D or 3D objects.
As they say, beauty lies in the eyes of beholder. For anything to look attractive to our eyes and soothing to our soul, it has to have a perfect anatomy.
Similarly even in gemstone carvings, jewelry or any likewise article, the anatomy of each element has to be flawless or absolute so as to look alluring and serene.