A system and method for base topology selection includes a network controller including a control unit and one or more ports coupled to the control unit and configured to couple the network controller to one or more network switching devices of a network. The network controller is configured to receive initiation messages from the network switching devices, receive configuration and status messages from the network switching devices, transmit discovery requests to the network switching devices, receive discovery responses from the network switching devices, determine a network topology of the network based on information associated with the initiation messages, the configuration and status messages, and the discovery responses, apply heuristic rules to the network topology, and select a base topology based on results of the applied heuristic rules. The network controller may further be configured to transmit flow control messages to the network switching devices to provision the network consistent with the selected base topology.