Most often, the type of medicine just only affects that part of the body, or affects it more strongly than elsewhere. It will be spread throughout the whole body but not do anything except in specific parts of the body.

Different parts of the body have different receptors (for naturally produced chemicals) that can interact with medications in different ways, and a big part of creating new medicines is finding chemicals that can interact with specific receptors in useful ways

edit: also, often a medication *will* work everywhere, you just won't notice in the parts of your body that don't have negative symptoms