The molecular Field-Coupled Nanocomputing (molFCN) paradigm encodes digital information in the charge distribution of molecules. The information propagates through electrostatic coupling within molecules, permitting minimal power consumption. Although the promising results in the design of molFCN circuits, a prototype is missing. Therefore, this work moves toward molFCN fabrication by presenting a methodology combining Finite Element Modelling with the SCERPA tool, boosting the simulation accuracy by considering both molecule and device physics. First, this work analyzes nano-trench-based molFCN single-line wires, examining information propagation dependencies on the nano-trench geometries. Then, the analysis of nano-trench-based multi-line wires points out the primary prototype specification to achieve this advantageous molFCN solution. Finally, we demonstrate the nano-trench as a valuable solution to achieve the write-in mechanism. Overall, this paper paves the way for molFCN fabrication-aware simulations for future prototyping.