Unveiling In-Gap States and Majorana Zero Modes in Superconductor-Topological Insulator Bilayer model

Interfaces between topological insulators and superconductors are promising platforms for realizing Majorana zero modes (MZMs) via the superconducting proximity effect. We introduce a bilayer model consisting of the surface states of a three-dimensional topological insulator (3DTI) coupled to an $s$-wave superconductor and systematically study the role of interlayer tunneling strength ($t_\perp$). We find that increasing $t_\perp$ shifts the proximity-induced (PrI) gap minima away from the $Γ$-point, giving rise to momentum-selective interference patterns that manifest as spatial oscillations in the in-gap states. By introducing an antidot with a magnetic vortex in the SC layer, we investigate the nature of in-gap states including MZMs and Caroli-de Gennes-Matricon (CdGM) modes. With increasing hybridization strength, the energy separation between MZMs and CdGM states increases, enhancing the isolation of MZMs. Importantly, in the strong hybridization limit, the leading CdGM separation remains large inspite of the decrease in the PrI gap. Spin- and spatial-resolved wavefunction analysis reveals angular momentum asymmetries absent in conventional $s$-wave systems. A direct comparison with a standalone $s$-wave superconductor confirms the emergence of distinct $p$-wave-like features in the bilayer geometry. Our results provide experimentally relevant predictions for tuning the stability of MZMs and their differentiation from the CdGM modes in SC-3DTI heterostructures and offer a theoretical framework for probing unconventional superconductivity in engineered topological systems.