As discussed in the companion paper [J. B. Witkoskie and J. S. Cao, J. Chem. Phys. 121, 6361 (2004), preceding paper], quantitative extraction of information from single molecule experiments by several proposed indicators is difficult since the experiments only observe certain characteristics of the system, even though the indicators can contain all available information. This paper shows how one can circumvent the shortcomings of these indicators by combining information extracted from indicators with a numerical Bayesian statistical approach. The Bayesian approach determines the relative probability of various models reproducing the entire sequence of the single molecules trajectory, instead of binning and averaging over the data, which removes much of this information. (C) 2004 American Institute of Physics.