As the hard disk drive industry is transitioning from longitudinal (LMR) to perpendicular (PMR) recording, a new set of reliability challenges had to be overcome. In particular, the magnetic media structure, which relies on well-segregated grains of 6-10 nm diameter, can exhibit a rough structure, with peak-to-mean amplitude of 3-6 nm. In this paper, we will discuss how this topography could affect the overall reliability of the head-disk interface. In the first part, we will illustrate the loss of adequate coverage from the overcoat on PMR media, compared to the smoother LMR media, and we will attempt to quantify the topography in terms of its deviation from a Gaussian height distribution. Particular emphasis will be given to surface outliers and their removal during the burnishing process. The second part will be devoted to the lubricant preferential migration to the grain boundaries, driven by surface tension. It will be shown by an EELS line scan that the lubricant film is indeed thicker in the valleys between the grains, in agreement with surface tension driven redistribution. Finally, we will demonstrate that the Touchdown Height (TDH) of a PMR disk is $0.5 nm higher than its LMR counterpart, owing to its enhanced nano-roughness. Once recognized, these challenges can be overcome through a careful and thorough optimization of the various processing parameters, eventually leading to an overall reliability level equal or better than LMR media.