In this work, we study silicon nanowire synthesis via one-step metal-assisted chemical etching (MACE) on microstructured silicon surfaces with periodic pillar/cavity array. It is found that hydrogen gas produced from the initial anodic reaction can be trapped inside cavities and between pillars, which serves as a mask to prevent local etching, and leads to the formation of patterned vertically aligned nanowire array. A simple model is presented to demonstrate that such bubble entrapment is due to the significant adhesion energy barrier, which is a function of pillar/cavity geometry, contact angle, and nanowire length to be etched. The bubble entrapment can be efficiently removed when extra energy is introduced by sonication to overcome this energy barrier, resulting in nanowire growth in all exposed surfaces. This bubble-regulated MACE process on microstructured surfaces can be used to fabricate nanowire arrays with desired morphologies.