Recent interests in ultra-low concentration of nanoscale biosensors have introduced new types of fluid structure interaction (FSI) problems where molecular and electrokinetic phenomena must be effectively considered. This has motivated enthusiasm in the development of FSI-based tools capable of accounting for various physics. Pertinent to biosensors, the immersed molecular electrokinetic finite element method (IMEFEM) was developed to study three-dimensional motion and deformation of interacting objects immersed in a fluid at room temperature under an applied electric field [1, 2]. The IMEFEM framework incorporates fluctuating hydrodynamics [3] and electrokinetics [4] into the immersed finite element method (IFEM) [5], which is a finite element based formulation extended from the immersed boundary methods. I will present the technical details of the IMEFEM framework and provide several applications. Future insights on the applications will also be conveyed.