We develop a systematic coarse graining procedure for systems of $N$ qubits. We exploit the underlying geometrical structures of the associated discrete phase space to produce a coarse-grained version with reduced effective size. Our coarse-grained spaces inherit key properties of the original ones. In particular, our procedure naturally yields a subset of the original measurement operators, which can be used to construct a coarse discrete Wigner function. These operators also constitute a systematic choice of incomplete measurements for the tomographer wishing to probe an intractably large system.