We investigate the applicability of the Jarzynski equality for reconstructing the energy landscape from force measurements obtained in single molecular unbinding and friction experiments. We demonstrate that single-well molecular potentials, such as the Lennard-Jones potential, could be accurately recovered using a reasonable number of force traces (∼100) obtained for velocities which are experimentally accessible, v≈5-100nm s-1. The situation becomes more complex in the presence of potential barriers in the energy profile. These include the double-well and periodic potentials that we consider here. The slow convergence of the reconstruction procedure results from a large energy dissipation which occurs during jumps across the potential barriers. We suggest a modification of the reconstruction procedure which allows the recovering of the correct shape of the potential wells even in the presence of potential barriers. However, a reconstruction of the potential shape in the vicinity of potential maxima requires additional information.