This paper describes a reproducible method for μm precision alignment of polydimethylsiloxane (PDMS) microchannels with coplanar electrodes using a conventional mask aligner for lab-on-a-chip applications. It is based on the use of a silicon mold in combination with a PMMA sarcophagus for precise control of the parallelism between the top and bottom surfaces of molded PDMS. The alignment of the fabricated PDMS slab with electrodes patterned on a glass chip is then performed using a conventional mask aligner with a custom-made steel chuck and magnets. This technique allows to bond and align chips with a resolution of less than 2 μm.