Micromachining of a polydimethylsiloxane (PDMS) microstructure by wet chemical etching is explored for microelectromechanical systems (MEMS) and microfluidic applications. A 100 μm thick PDMS film was patterned with different microstructure designs by wet chemical etching using a N-methyl-2-pyrrolidone (C16H36FN) and tetra-n-butylammonium fluoride (C5H9NO) mixture solution with 3:1 volume ratio after lithography for studying etching characteristics. The patterning parameters, such as etch rate, surface roughness, pH of etchant solution with time, were thoroughly investigated. A detailed study of surface morphology with etching time revealed nonlinear behaviour of the PDMS surface roughness and etch rate. A maximum rate of 1.45 μm min-1 for 10 min etching with surface roughness of 360 nm was achieved. A new approach of wet chemical etching with pH controlled doped etchant was introduced for lower surface roughness of etched microstructures, and a constant etch rate during etching. Variation of the etching rate and surface roughness by pH controlled etching was performed by doping 5-15 gm l-1 of silicic acid (SiO2xH2O) into the traditional etchant solution. PDMS etching by silicic acid doped etchant solution showed a reduction in surface roughness from 400 nm to 220 nm for the same 15 μm etching. This study is beneficial for micromachining of various MEMS and microfluidic structures such as micropillars, microchannels, and other PDMS microstructures. © 2016 IOP Publishing Ltd.