Quasiparticle interference (QPI) imaging is a powerful tool for the study of the low-energy electronic structure of quantum materials. However, the measurement of QPI by scanning tunneling microscopy (STM) is restricted to surfaces and is thus inherently constrained to two dimensions. QPI has proved immensely successful for the study of materials that exhibit a quasi-two-dimensional electronic structure, yet it raises questions about how to interpret QPI in materials that have a highly three-dimensional electronic structure. In this paper, we address this question and establish the methodology required to simulate and understand QPI arising from three-dimensional systems as measured by STM. We calculate the continuum surface Green's function in the presence of a defect, which captures the role of the surface and the vacuum decay of the wave functions. We find that defects at different depths from the surface will produce unique sets of scattering vectors for three-dimensional systems, which nevertheless can be related to the three-dimensional electronic structure of the bulk material. We illustrate the consequences that the three-dimensionality of the electronic structure has on the measured QPI for a simple cubic nearest-neighbor tight-binding model, and then demonstrate application to a real material using a realistic model for PbS. Our method unlocks the use of QPI imaging for the study of quantum materials with three-dimensional electronic structures and introduces a framework to generically account for kz dispersions within QPI simulations.