Harnessing the exotic properties of molecular level nanostructures to produce novel sensors, metamaterials, and futuristic computer devices can be technologically transformative. In addition, connecting the molecular nanostructures to ferromagnetic electrodes bring the unprecedented opportunity of making spin property based molecular devices. We have demonstrated that magnetic tunnel junction based molecular spintronics device (MTJMSD) approach to address numerous technological hurdles that have been inhibiting this field for decades (P. Tyagi, J. Mater. Chem., Vol. 21, 4733). MTJMSD approach is based on producing a capacitor like a testbed where two metal electrodes are separated by an ultrathin insulator and subsequently bridging the molecule nanostructure across the insulator to transform a capacitor into a molecular device. Our prior work showed that MTJMSDs produced extremely intriguing phenomenon such as room temperature current suppression by six orders, spin photovoltaic effect, and evolution of new forms of magnetic metamaterials arising due to the interaction of the magnetic a molecule with two ferromagnetic thin films. However, making robust and reproducible electrical connections with exotic molecules with ferromagnetic electrodes is full of challenges and requires attention to MTJMSD structural stability. This paper focuses on MTJMSD stability by describing the overall fabrication protocol and the associated potential threat to reliability. MTJMSD is based on microfabrication methods such as (a) photolithography for patterning the ferromagnetic electrodes, (b) sputtering of metallic thin films and insulator, and (c) at the end electrochemical process for bridging the molecules between two ferromagnetic films separated by ∼ 2nm insulating gap. For the successful MTJMSD fabrication, the selection of ferromagnetic metal electrodes and thickness was found to be a deterministic factor in designing the photolithography, thin film deposition strategy, and molecular bridging process. We mainly used isotropic NiFe soft magnetic material and anisotropic Cobalt (Co) with significant magnetic hardness. We found Co was susceptible to chemical etching when directly exposed to photoresist developer and aged molecular solution. However, NiFe was very stable against the chemicals we used in the MTJMSD fabrication. As compared to NiFe, the Co films with > 10nm thickness were susceptible to mechanical stress-induced nanoscale deformities. However, cobalt was essential to produce (a) low leakage current before transforming the capacitor from the magnetic tunnel junction into molecular devices and (b) tailoring the magnetic properties of the ferromagnetic electrodes. This paper describes our overall MTJMSD fabrication scheme and process optimization to overcome various challenges to produce stable and reliable MTJMSDs. We also discuss the role of mechanical stresses arising during the sputtering of the ultrathin insulator and how to overcome that challenge by optimizing the insulator growth process. This paper will benefit researchers striving to make nanoscale spintronics devices for solving grand challenges in developing advanced sensors, magnetic metamaterials, and computer devices.