Abstract LabVIEW™ is steadily gaining in popularity as the programming language of choice for scientific data acquisition and control. This is due to the vast array of measurement instruments and data acquisition cards supported by the LabVIEW™ environment, and the relative ease with which advanced software can be programmed. Furthermore, virtual instruments that are designed for a given system can be easily ported to other LabVIEW™ platforms and hardware. This paper describes the new LabVIEW™ based scanning and control system developed specifically for proton beam micromachining (PBM) applications. The new system is capable of scanning figures at 16-bit resolution with improved sub-microsecond scan rates. Support for electrostatic beam blanking and external dose normalization using a TTL signal have been implemented. The new software incorporates a semi-automated dose calibration system, and a number of novel dose normalization methods. Limitations of the current beam scanning hardware are discussed in light of new results obtained from micromachining experiments performed in SU-8 photoresist.