Two independent biological replicates of estrogen depletion were employed with differing drug treatment conditions. Data Set I consisted of 9-month-old New Zealand white female rabbits treated as follows: sham-operated (n=11), ovariectomized (OVX; n=12), OVX+200 μg kg−1 alendronate (ALN), 3 × a week for 27 weeks (n=12) and OVX+10 mg kg−1 Cathepsin-K inhibitor (CatKI) daily for 27 weeks. Data Set II consisted of 6-month-old New Zealand white female rabbits that were sham-operated (n=12), OVX (n=12) or OVX+0.05 mg kg−1 17β-estradiol (ERT) 3 × a week for 13 weeks (n=12). Samples from the cortical femur were polished and demineralized to make them suitable for atomic force microscopy (AFM) imaging. Type I collagen fibrils present in bundles or sheets, running parallel to each other, were combined into a class termed Parallel. Fibrils present outside of such structures, typically in images with an angular range of non-parallel fibrils, were combined into a class termed Oblique. The percentage of fibrils coded as Parallel for Sham animals in Data Sets I and II was 52% and 53%, respectively. The percentage of fibrils coded as Parallel for OVX animals in Data Sets I and II was 35% in both cases. ALN and ERT drug treatments reduced the change from 18 to 12%, whereas CatKI treatment reduced the change to 5%.