The structure of a free flexible macromolecule confined in a cylindrical nanopore whose wall is coated by a polymer brush is studied by Monte Carlo simulation, varying the grafting density as well as the radius of the cylindrical pore. Because of this confinement, the free chain is stretched in axial direction; while for small grafting densities of the brush the end-to-end distance increases monotonously with decreasing pore radius, a nonmonotonic variation occurs for larger grafting densities. We show that this effect is due to strong interpenetration of the free chain and the brush chains; for very narrow pores a strong layering of cylindrical shells is found, and comparison with self-consistent field calculations (SCF) shows that the latter can predict the nonmonotonic variation in qualitative accord with the simulation. The robustness of the SCF approach is then used to demonstrate the occurrence of the observed "penetration transition" in a broader range of chain lengths and grafting densities.