The disclosure describes a method and system that allows a user to configure electrical stimulation therapy by selecting a structure of an anatomical region represented by an atlas. The atlas is a reference anatomical region of a reference anatomy that a clinician may use to identify structures of a patient anatomy that the clinician desires to stimulate during therapy. Selecting structures from the atlas may not provide the most efficacious stimulation therapy to the patient because of slight differences between the atlas and the patient anatomical region approximated by the atlas. However, structure selection may be efficient for the clinician, and allow the system to generate stimulation parameters that are adequate to treat the patient. The atlas may be most suitable for both axi-symmetric or three-dimensional leads having a complex electrode array geometry that allow greater flexibility in creating stimulation fields.