A method of filling a prescription using a pharmaceutical storage and retrieval device, the pharmaceutical storage and retrieval device including a housing, an interface panel supported by the housing and having an access control device, a shelving system supported by the housing and including a plurality of shelves, an access port supported by the housing and including a platform, a door supported by the housing to selectively cover the access port, a scanner supported by the housing and included with the platform, and a gantry system positioned within the housing, the gantry system including a gripper assembly and a motor (864, 866, 869) coupled to the gripper assembly to move the gripper assembly within the housing, the method comprising: verifying, by a processor, identification information input into the access control device; obtaining, by the processor, a queue of prescriptions to be filled from a pharmacy computer; selecting a prescription from the queue of prescriptions to be filled, the selected prescription containing prescription information including a medication type; determining, by the processor, a shelf location of a container expected to have the medication type of the prescription information; retrieving the container from the determined shelf location in the shelving system by engaging the container with the gripper assembly of the gantry system; positioning the container on the platform within the access port by moving the gripper assembly and the container to the access port with the motor (864, 866, 869) of the gantry system; scanning, by the scanner, the container to determine an actual medication type within the container while the container is on the platform of the access port; opening the door to the access port if the actual medication type within the container matches the medication type of the prescription information; and returning the container to its shelf location if the actual medication in the container does not match the medication type of the prescription information. verifying, by a processor, identification information input into the access control device; obtaining, by the processor, a queue of prescriptions to be filled from a pharmacy computer; selecting a prescription from the queue of prescriptions to be filled, the selected prescription containing prescription information including a medication type; determining, by the processor, a shelf location of a container expected to have the medication type of the prescription information; retrieving the container from the determined shelf location in the shelving system by engaging the container with the gripper assembly of the gantry system; positioning the container on the platform within the access port by moving the gripper assembly and the container to the access port with the motor (864, 866, 869) of the gantry system; scanning, by the scanner, the container to determine an actual medication type within the container while the container is on the platform of the access port; opening the door to the access port if the actual medication type within the container matches the medication type of the prescription information; and returning the container to its shelf location if the actual medication in the container does not match the medication type of the prescription information.