Phononic crystals (PnC) with a specifically designed defect have been recently introduced as novel sensor platform. Those sensors feature a band gap covering the typical input span of the measurand as well as a narrow transmission peak within the band gap where the frequency of maximum transmission is governed by the measurand. This innovative approach has been applied for determination of compounds in liquids . Improvement of sensitivity requires higher probing frequencies around 100 MHz and above. In this range surface acoustic wave devices (SAW) provide a promising basis for PnC based microsensors . The respective feature size of the PnC SAW sensor has dimensions in the range of 100 μm and below. Whereas those dimensions are state of the art for common MEMS materials, etching of holes and cavities in piezoelectric materials having an aspect ratio diameter/depth is challenging. In this contribution we describe an improved technological process to manufacture considerably deep and uniform phononic crystal structures inside of SAW substrates.