Brain-computer interfaces (BCIs) use brain signals to convey a user's intent. Some BCI approaches begin by decoding kinematic parameters of movements from brain signals, and then proceed to using these signals, in absence of movements, to allow a user to control an output. Recent results have shown that electrocorticographic (ECoG) recordings from the surface of the brain in humans can give information about kinematic parameters (e.g., hand velocity or finger flexion). The decoding approaches in these demonstrations usually employed classical classification/regression algorithms that derive a linear mapping between brain signals and outputs. However, they typically only incorporate little prior information about the target kinematic parameter. In this paper, we show that different types of anatomical constraints that govern finger flexion can be exploited in this context. Specifically, we incorporate these constraints in the construction, structure, and the probabilistic functions of a switched non-parametric dynamic system (SNDS) model. We then apply the resulting SNDS decoder to infer the flexion of individual fingers from the same ECoG dataset used in a recent study. Our results show that the application of the proposed model, which incorporates anatomical constraints, improves decoding performance compared to the results in the previous work. Thus, the results presented in this paper may ultimately lead to neurally controlled hand prostheses with full fine-grained finger articulation.