This article describes a novel assembly technique with highly accurate semi-automatic alignment of polydimethylsiloxane (PDMS) substrates for microfluidic devices. The technique is realized by specific concave structures, consisting of fringes of PDMS named the "Pliant Zipper". Microchannels and the Pliant Zipper are easily fabricated together by soft lithography. Applying two Pliant Zippers on different substrates enables them to be engaged semi-automatically in the alignment position. The aligned substrates are held tightly without any external support. Highly accurate alignment was achieved manually without the micro-adjustment required in conventional techniques. The experiments presented in this article demonstrate the high accuracy of the alignment. The misalignment range of the experiments is less than 1.9 μm.