The approach of monolithic 3D IC (M3D) integration using monolithic inter-tier-vias (MIVs) as interconnect structures is considered. Although, M3D ICs show many benefits of heterogeneous integration without significant area overhead compared to 3D ICs, reliability and thermal issues become daunting challenges to be addressed. Hence, this study focuses on electromigration issues of current density, thermal stress, and structure deformation due to temperature loading. For the analysis Cu and carbon nanotube (CNT) filler materials were chosen in MIV structure. Our analysis reveals that CNT based MIV offers two-fold higher current density and 91% lesser thermal stress compared to Cu based MIVs. Furthermore, at different voltage values, the current density profiles are examined. For the comprehensive investigations of structure deformations, temperature gradient was allowed at the ends of the MIV structure. The results show less deformations in CNT compared to Cu, based on the stress induced among them. The failure time prediction shows higher mean time to failure value of CNT based MIV than Cu based MIV.