We present experimental and theoretical results concerning the forced filling and spontaneous drying of hydrophobic cylindrical mesopores in the dynamical regime. Pores are structured with organic/inorganic moieties responsible for a periodicity of the surface energy along their axis. We find that the forced intrusion of water in these hydrophobic pores presents a slow dynamics: the intrusion pressure decreases as the logarithm of the intrusion time. We find that this slow dynamics is well described quantitatively by a classical model of activated wetting at the nanoscale, giving access to the structural length scales and surface energies of the mesoporous material.