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Several parameter estimation problems (or ''inverse'' problems) such as those that occur in hydrology and geophysics are solved using partial differential equation (PDE)-based models of the physical system in question. Likewise, these problems are usually underdetermined due to the lack of enough data to constrain a unique solution. In this paper, we present a framework for the solution of underdetermined inverse problems using COMSOL Multiphysics (formerly FEMLAB) that is applicable to a broad range of physical systems governed by PDEs. We present a general adjoint state formulation which may be used in this framework and allows for faster calculation of sensitivity matrices in a variety of commonly encountered underdetermined problems. The aim of this approach is to provide a platform for the solution of inverse problems that is efficient, flexible, and not restricted to one particular scientific application. We present an example application of this framework on a synthetic underdetermined inverse problem in aquifer characterization, and present numerical results on the accuracy and efficiency of this method. Our results indicate that our COMSOL-based routines provide an accurate, flexible, and scalable method for the solution of PDE-based inverse problems.