A method and software interface enables selective processing of data transmissions containing one or more medication orders intended for a pharmacy. Data transmissions are monitored and parsed for prescribed information which is utilized to populate a prescribed data structure. The data structure and parsing rules can be associated with a specific source that can be determined from the data transmission. The parsed data is tested against an order database to determine suitability for automated handling. If suitable, the medication preparation system prepares the medications identified by the data. Those portions of the data that are not suited for automated handling are released (e.g., from the parser). Further verification can be performed by determining the source of the data transmission and verifying it as a valid source. Data transmissions can be monitored over a network, within a network component, or in cooperation with another software program.