The beam orientation optimization (BOO) problem for intensity-modulated radiation therapy (IMRT) is the selection of beams for radiation delivery. Conventionally, it is desirable for beams to be spatially separated to ensure a homogeneous dose. However, many BOO approaches yield clustered beams. This issue is especially prevalent for total marrow irradiation (TMI), where the target is very large and spread throughout the patient’s body. Based on previous set-cover formulations of the BOO problem for TMI-IMRT, we propose an extension that enforces geometric beam constraints by iteratively removing beams violating geometric constraints within the set-cover framework. After beams are selected, they are used as input to a fluence map optimization solver to obtain optimal fluence maps. Results for a clinical TMI case meet clinical guidelines for target coverage and differentiation of organ and target doses.