The data pack provides helium atom microscope image data for a test sample of FIB-ed trenches in silicon and of an Alvetex scaffold along with simulated ray tracing images for the same test sample. Optical profiler and SEM images are also provided that were used to measure the depth of the trenches. Text description files are included within the archive. The research was supported by EPSRC grants EP/R008272/1 and EP/R008051/1, as well as a Mathworks Ltd. studentship and a Leverhulm visiting professorship