A method and system is provided for emulating individual JTAG devices in a multiple device boundary scan chain. The method includes coupling an emulator to the scan chain, and obtaining the topology of the scan chain. One device within the scan chain is then selected, and at least one other device within the scan chain is placed into bypass mode. Emulation instructions are sent to the scan chain, so that the emulation instructions bypass the at least one other device and are executed by the one device.