System and method for managing routing of data in a distributed computing system, such as a distributed computing system that uses PCI Express protocol to communicate over an I/O fabric. A physical tree that is indicative of a physical configuration of the distributed computing system is determined, and a virtual tree is created from the physical tree. The virtual tree is then modified to change an association between at least one source device and at least one target device in the virtual tree. A validation mechanism validates the changed association between the at least one source device and the at least one target device to enable routing of data from the at least one source device to the at least one target device.