Habitat structural complexity is created by biotic and abiotic processes that operate over a range of scales. This can be seen clearly on coral reefs, where corals and reef geomorphology create structure from mm to km scales. Here, we quantified the relative contribution of biotic and abiotic structures to habitat complexity using ‘Structure from Motion’, a technology that allows accurate 3D models of environments to be reconstructed from overlapping photographs. We calculated the linear fractal dimension of these models using a virtual analogue of a profile gauge. By adjusting the spacing between profile gauge rods, we partitioned structural complexity into a series of scale intervals. We identified scales that were most indicative of coral cover (0.5-16 cm) and reef geomorphology (16-256 cm). We found that reefs in the Main Hawaiian Islands have more complexity at finer scales than reefs in the Northwest Hawaiian Islands, which we attribute to the latitudinal gradient in coral cover along the archipelago. At coarser scales, islands at each end of the archipelago have sites with high structural complexity, with less complexity in the center of the archipelago. These differences are consistent with geologic factors shaping island uplift, subsidence, and reef formation. In addition, we found that different coral genera and morphologies display unique patterns of fractal dimension, with branching Porites corals creating the greatest amount of habitat structure at nearly all scales. This study demonstrates how multi-scale approaches can be used to identify the processes responsible for reef structural complexity and changes in structure over time.