Structure, anatomy, framework, skeleton are often used interchangeably.
Structure is by far the richest in implications and the widest in its range of application. In general it denotes the formation, arrangement, and articulation of parts in something built up by nature or made by man. Often the word implies reference to everything that enters into the makeup of a particular body, organism, edifice, fabric, or substance; thus, a study of the structure of a brain involves attention to the two kinds of matter (gray and white) of which it is composed, to the three parts (forebrain, midbrain, hindbrain) into which it is divided, to the subdivisions of each of these parts, to the connections and interrelations between all these divisions, and to any peculiarities in form or arrangement of parts.
Sometimes, however, structure implies a reference to certain features only, as for example: the parts or elements which distinguish kinds rather than individuals or the parts or features which are essential or necessary to a thing’s existence as distinguished from those that are removable, detachable, or dispensable or the parts or features that reveal the underlying design as opposed to those that complete the work or bring it into fullness of being.
Anatomy may be preferred when the typical structure of an organism or of an organ is to be denoted.
Framework and skeleton are applied to the underlying or supporting structure.
Framework is used chiefly in reference to an artificial construction which serves as a prop and a guide in building but which is not visible in the completed thing.
Skeleton is frequently used in the building trades for a rigid framework, especially one made of steel; it is often used in place of structure , design , outline in reference to literary constructions, sometimes to imply that the design is carefully developed and its parts definitely articulated, but more often, probably, to indicate a sketchy conception of the whole which serves as a starting point. In either case it is usually further implied that the writing out in literary form and the elaboration of atmosphere, details, characters remain to be accomplished.