Dynamic elastography, whether based on magnetic resonance, ultrasound, or optical modalities, attempts to reconstruct quantitative maps of the viscoelastic properties of biological tissue, properties altered by disease and injury, by noninvasively measuring mechanical wave motion in the tissue. Most reconstruction strategies that have been developed neglect boundary conditions, including quasi-static tensile or compressive loading resulting in a nonzero prestress. Significant prestress is inherent to the functional role of some biological tissues currently being studied using elastography, such as skeletal and cardiac muscle, arterial walls, and the cornea. In the present article a configuration, inspired by muscle elastography but generalizable to other applications, is analytically and experimentally studied. A hyperelastic polymer phantom cylinder is statically elongated in the axial direction while its response to transverse-polarized vibratory excitation is measured. We examine the interplay between uniaxial prestress and waveguide effects in this muscle-like tissue phantom using computational finite element simulations and magnetic resonance elastography measurements. Finite deformations caused by prestress coupled with waveguide effects lead to results that are predicted by a coordinate transformation approach that has been previously used to simplify reconstruction of anisotropic properties using elastography. Here, the approach estimates material viscoelastic properties that are independent of the nonhomogeneous prestress conditions without requiring advanced knowledge of those stress conditions.