Experimental investigations into the effect of duty cycle and electrolyte concentration on the surface topography in the microchannel formation in the soda-lime glass substrate by a pulsed electrochemical discharge machining are reported. These microstructures are required in various microsystems applications such as microfluidics, integrated-passive-devices for radio-frequency MEMS, 3-D glass interposer. No significant machining happened at lower duty cycles (< 50%) and lower electrolyte concentration (10%), which was due to the lower surface temperature generated as predicted by the numerical simulation. At these parameters, the tool electrode locally adhered to the glass substrate and prevented the underneath glass surface from being etched periodically. The non-homogeneous etching leads to the uneven surface topography and pillar-like structures, which is termed as the 'localized adhesion and fast releasing effect. It was observed to be severe when the tool electrode was in contact with the glass substrate, i.e., zero-gap. At this condition, high temperature led to the thermal expansion of the tool electrode, which resulted in the intermittent machining and pillar-like structures in the middle of the microchannel. As the gap was increased, this effect was subsidized, and the surface topography of microchannel improved. Variation in microchannel depth and heat-affected zone (HAZ) at various electrolyte concentrations and duty cycles were investigated. Experimental results revealed that the microchannel depth and the HAZ increase with an increase in the duty cycle and electrolyte concentration. Deeper microchannels (> 500 mu m) having complex shapes were demonstrated by using a multi-pass milling technique. The capability of the presented method in making buried redistribution lines in 3D MEMS inductor is also shown.