In this paper, we present a Bayesian approach for spectral unmixing of multispectral Lidar (MSL) data associated with surface reflection from targeted surfaces composed of several known materials. The problem addressed is the estimation of the positions and area distribution of each material. In the Bayesian framework, appropriate prior distributions are assigned to the unknown model parameters and a Markov chain Monte Carlo method is used to sample the resulting posterior distribution. The performance of the proposed algorithm is evaluated using synthetic MSL signals, for which single and multi-layered models are derived. To evaluate the expected estimation performance associated with MSL signal analysis, a Cramer-Rao lower bound associated with model considered is also derived, and compared with the experimental data. Both the theoretical lower bound and the experimental analysis will be of primary assistance in future instrument design.