A selectively transparent bridge facilitates a PCI device presenting itself to the host as a PCI-to-PCI bridge but selectively hiding and isolating hardware from the host bus. PCI configuration may be achieved through the standard PCI Express configuration mechanisms, but instead of configuring devices directly, a configuration processor in the selectively transparent bridge may intercept the configuration packets from the host, and create a virtual configuration to alter how the bus topology appears to the host. Devices are selectively hidden and managed by the configuration processor, resulting in simplified complexity and bus depth. Since the selectively transparent bridge appears to the host as a transparent bridge, no special drivers or resource preallocations are required, although the selectively transparent bridge fully supports special drivers and/or resource preallocations. Devices located/connected downstream of the bridge may therefore function with unmodified drivers.