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High Q-factor open-box mode resonances have been found in the microwave measurements of several 3-D printed dielectric-filled metal-pipe rectangular waveguides (MPRWGs). These parasitic Fabry-Pérot eigenmodes are confined by the conductive walls in the transverse plane of the MPRWG and partially confined by the air-dielectric and dielectric-air boundaries in the longitudinal direction. The excitation of open-box modes was previously speculated to be due to the inhomogeneous and/or anisotropic nature of the 3-D printed dielectric-fillers. This has now been confirmed, by representing the inhomogeneous and anisotropic nature of the woodpile-like dielectric structure (physical realm), with an anisotropic dielectric constant tensor (simulation realm). Analytical and numerical eigenmode solvers, previously used by the authors with MPRWGs, are applied here to parallel-plate waveguides (PPWGs) and circular waveguides (CWGs); identifying all the individual parasitic open-box modes. With the former, its TM₁₁ mode exhibits an ultra-high Q-factor of approximately 2,300 at X-band, which is considerably higher than those found with other modes and in other waveguide structures. Finally, a numerical full-wave frequency-domain simulator that employs the dielectric constant tensor is introduced in this paper. This new modeling technique independently confirms that open-box modes are excited in 3-D printed dielectric-filled MPRWG, PPWG and CWG structures. This paper provides the foundations for accurately modeling parasitic resonances associated with inhomogeneities and anisotropy in 3-D printed microwave components; not just the metal-walled waveguide structures considered here, but the methodology could also be extended to generic 3-D printed dielectric waveguides and substrate-based transmission lines.