We present a spiking neuron brain model implemented in 318,870 LIF neurons organized with distinct cortical modules, a basal ganglia, and a thalamus, that is capable of flexibly following memorized commands. Neural activity represents a structured set of rules, such as “If you see a 1, then push button A, and if you see a 2, then push button B”. Synaptic connections between these neurons and the basal ganglia, thalamus, and other areas cause the system to detect when rules should be applied and to then do so. The model gives a reaction time difference of 77 ms between the simple and two-choice reaction time tasks, and requires 384 ms per item for sub-vocal counting, consistent with human experimental results. This is the first biologically realistic spiking neuron model capable of flexibly responding to complex structured instructions.