A new surface micromachining technique for Poly dimethylsiloxane (PDMS) microchannels has been developed to address the leakage problem affecting traditional PDMS microchannel process with embedded tall structures or sudden topographical transitions. Bulk micromachined PDMS cannot be conformally bonded with the surfaces having tall topological features such as thick film electrodes, porous reactor beds and other structural features. Surface micromachining technique with PDMS as structural material and photoresist as a sacrificial material allows the creation of PDMS microchannels on substrates with significant topography. Adhesion of the structural layer with the substrate was characterized for different prepolymer ratios using standard tensile test and 1:3 (Curing agent: base) combination was found to be the best with maximum adhesion strength of 7.5 MPa. The effectiveness of this technique is demonstrated by the fabrication of microchannels with embedded 6μm thick Silver electrodes. The microchannels were leak proof and conformal contact between the PDMS and electrode was confirmed through SEM. The release time for microchannels was reduced to 1 min irrespective of the length of the microchannel. The extension of this technique for fabrication of multi layered microchannel structure was demonstrated through a microfluidic valve. The valve closure occurred at 6.37 kPa.