IEEE Std. 1687, or IJTAG, defines flexible serial scan-based architectures for accessing embedded instruments efficiently. In this paper, we present a novel test architecture that employs IEEE Std. 1687 together with an efficient test controller to carry out 3D-IC testing autonomously. The test controller can deliver parallel test data for the IEEE Std. 1687 structures and the cores under test, and provide required control signals to control the whole test procedure. This design can achieve at-speed, autonomous and programmable testing in 3D-ICs. Experimental results show that the additional area and test cycle overhead of this architecture is small considering its autonomous test capability.