Using atom beams to image the surface of samples in real space is an emerging technique that delivers unique contrast from delicate samples. Here, we explore the contrast that arises from multiple scattering of helium atoms, a specific process that plays an important role in forming topographic contrast in scanning helium microscopy (SHeM) images. A test sample consisting of a series of trenches of varying depths was prepared by ion beam milling. SHeM images of shallow trenches (depth/width < 1) exhibited the established contrast associated with masking of the illuminating atom beam. The size of the masks was used to estimate the trench depths and showed good agreement with the known values. In contrast, deep trenches (depth/width > 1) exhibited an enhanced intensity. The scattered helium signal was modeled analytically and simulated numerically using Monte Carlo ray tracing. Both approaches gave excellent agreement with the experimental data and confirmed that the enhancement was due to localization of scattered helium atoms due to multiple scattering. The results were used to interpret SHeM images of a bio-technologically relevant sample with a deep porous structure, highlighting the relevance of multiple scattering in SHeM image interpretation.