Background: Several high-precision stereotactic radiation therapy modalities are currently used in clinical settings. We aimed to evaluate whether the CyberKnife (CK) or TrueBeam (TB) radiation treatment systems were more appropriate for treating targets of various morphologies according to the physical properties of each device.  Materials and Methods: Spheres (diameter = 5–50 mm), as well as triangular prisms and cubes (length of a side = 10–50 mm), were used as virtual targets for each treatment delivery system. A phantom with dosimetry film was irradiated to evaluate the flatness and gradient of the radiation treatment from each modality. Results: The homogeneity index (HI) for the spherical targets was significantly higher (dose distribution was more homogeneous) using the TB than when using the CK (1.9 vs. 1.4; p = 0.002). There were no significant differences between treatment modalities in the HI for more complex shapes. The HI increased monotonically as the virtual target diameter increased for the CK (p = 0.048). The flatness parameter was lower for the TB than for the CK (1.4 vs. 1.1; p < 0.001). Conclusion: The CK is particularly robust for delivering therapeutic radiation to small targets, while the TB is more suitable for targets with a simple shape or when the HI is a critical treatment factor.