Energetic protons, neutrons, and heavy ions undergoing collisions with target nuclei of varying Z can produce residual heavy recoil fragments via intra‐nuclear cascade/evaporation reactions. The particles produced in these non‐elastic collisions generally have such extremely short range (∼<10 μm) that they cannot be directly observed by conventional detection methods including CR‐39 plastic nuclear track detector (PNTD) that has been chemically etched for analysis by standard visible light microscopy. However, high‐LET recoil fragments having range on the order of several cell diameters can be produced in tissue during radiotherapy using proton and carbon beams. We have developed a method to analyze short‐range, high‐LET tracks in CR‐39 plastic nuclear track detector (PNTD) using short duration chemical etching (∼<1 μm) following by automated atomic force microscope (AFM) scanning. The post‐scan data processing used in this work was based on semi‐automated matrix analysis opposed to traditional grey‐scale image analysis. This method takes advantage of the 3‐D data obtained via AFM to achieve robust discrimination of nuclear tracks from other features inherently present in the post‐etch detector surface. Through automation of AFM scanning, sufficient AFM scan frames were obtained to attain an LET spectrum spanning the LET range from 200–1500 keV/μm. In addition to our experiments, simulations were carried out with the Monte Carlo transport code, FLUKA. To demonstrate this method, CR‐39 PNTD was exposed to the proton therapy beam at Loma Linda University Medical Center (LLUMC) at 60 and 230 MeV. Additionally, detectors were exposed to 1 GeV protons at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). For these exposures CR‐39 PNTD, Al and Cu target foils were used between detector layers.

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