In this paper, an approach for 3D plasma structure diagnostics using tomographic optical emission spectroscopy (Tomo-OES) of a nanosecond pulsed atmospheric pressure plasma jet (APPJ) is presented. In contrast to the well-known Abel inversion, Tomo-OES does not require cylindrical symmetry to recover 3D distributions of plasma light emission. Instead, many 2D angular projections are measured with intensified cameras and the multiplicative algebraic reconstruction technique is used to recover the 3D distribution of light emission. This approach solves the line-of-sight integration problem inherent to optical diagnostics, allowing recovery of localized OES information within the plasma that can be used to better infer plasma parameters within complex plasma structures. Here, Tomo-OES was applied to investigate an APPJ operated with helium in ambient air and impinging on planar and structured dielectric surfaces. Surface charging caused the guided streamer from the APPJ to transition to a surface ionization wave (SIW) that propagated along the surface. The SIW experienced variable geometrical and electrical material properties as it propagated, leading to complex 3D configurations that were non-symmetric and spatially complex. Light emission from He, N2+, and N2 were imaged at ten angular projections and the respective time-resolved 3D emission distributions in the plasma were then reconstructed. The spatial resolution of each tomographic reconstruction was 7.4 um and the temporal resolution was 5 ns, sufficient to observe the guided streamer and the effects of the structured surface on the SIW. In ambient air, Penning ionization of N2 leads to a ring or outer layer of N2+ that spatially converges to form the “plasma bullet.” The SIW enters trenches of size 150 um, leading to decreases in plasma light emission in regions above the trenches. The plasma light emission is higher in some regions with trenches, possibly due to effects of field enhancement.