I've seen the word 'proper' in websites, lectures, etc., in the context of human anatomy. But I'm unsure as to what its definition is. For example, the 'oral cavity proper'.
This use of proper is simply using one of the normal English meanings of the adjective proper: "In the very strictest sense of the word or phrase". Thus, while 'oral cavity' generally might be taken to include, in part, the space between the cheeks and the teeth, the term 'oral cavity proper' refers to a stricter definition which excludes that space.