A prototype STM system with high aspect ratio measurement capability is developed to fulfill accurate profile measurement of a high step microstructure with 90° steep sidewall. Distinguished from the traditional STM, the new system consists of a long range piezoelectric (PZT) actuator with full stroke of 60 μm as Z-direction servo scanner, a specially customized high aspect ratio STM probe with effective tip length of 300 μm, and an X-Y motorized driven stage for planar scanning. A tilt stage is used to adjust the probe-sample relative angle to compensate the evitable non-parallel effects. Based on the new STM system, sample-tilt-scanning methodology is proposed for eliminating the scanning blind region between the probe and the microstructure. A high step microstructure with height of 23 μm, 90° steep sidewall and width of 50μm has been successfully measured. The slope angle of the sidewall has been achieved to be 85° and the step height at the rising edge and the trench depth at the falling edge are both measured to be 22.96 μm. The whole measuring process only spent less than 10 min. It provides an effective and nondestructive solution for the measurement of high step or deep trench microstructures. In addition, this work also opens the way for further study on sidewall roughness and the tip-sample interaction at the edge of the sidewall, which are highly valuable for fabrication and quality control of high step microstructures.