The Variational Implicit Solvent Model (VISM) is a theoretical and computational framework for studying bimolecular systems with complex topology. Central in VISM is an effective free-energy of all possible interfaces separating solutes (e.g., proteins) from solvent (e.g., water). Such a functional can be minimized numerically by a level-set method to determine the stable equilibrium conformations and solvation free energies. In this talk we introduce two numerical methods related to VISM. The first one is the Compact Coupling Interface Method (CCIM), which is a finite difference method for elliptic interface problems with accurate gradient approximation. The second one is the Binary Level Set-VISM, which is coupled with the Monte Carlo method to simulate the binding of biomolecules.