Super-resolution photonic nanojet interferometry is a new modality for 3D label-free super-resolution imaging. We present a comparative study of the photonic nanojet interaction with a polymer sample. We use numerical modelling to understand the interaction between a microsphere-induced photonic nanojet and the polymer sample. The numerical model employs the same set of input parameters (melamine formaldehyde microsphere with a diameter of 11 μm and a refractive index of 1.68), as in our experiments. The interaction is described using the Finite-Difference Time-Domain method applied on a finely discretized mesh. The knowledge gained using the verified and validated model, will be used to conduct numerical simulations in a wider parameter space. This enables optimizing the design of 3D-interferometric super-resolution microscopes.