Abstract Two-dimensional nanomaterials have emerged as next generation electronic materials due to their electrical and thermal properties. This article presents a detailed comparative analysis of two biosensing field-effect transistors (FETs) based on molybdenum disulphide (MoS2). While one architecture is based on the conventional MoS2-FET, the other one is a trench-MoS2-FET. The article establishes a method to extract design parameters which can appropriately model a MoS2-based FET for biosensing applications on industrial device simulators. The electrical parameters are reported for different biomolecule concentration and gate dielectric materials.