We have used coarse-grained molecular dynamics simulations to study the boundary condition for the grafting density in good and poor solvents. In a good solvent investigated the dependence of the boundary condition on the stagnation length for flow within the brush scales with the distance between chains D in accordance with the Alexander-de Gennes prediction for the brush height, as D-2/3, while the flow of a simple Newtonian liquid over a polymer brush. We height itself scales as D-2 due to a short chain length. In a poor solvent the polymer chains undergo constrained dewetting on the surface to form nanoscale patterns of polymer aggregates. When the boundary condition for flow at the polymer differs from that at the underlying substrate, patterns emerge in the flow, such that the liquid near the surface flows at different rates over the polymer and substrate. We have applied a simple model to relate the boundary condition at these patterned surfaces to the height and surface coverage of the polymer aggregates.