Surface morphology of the MgO layer and magnetic properties of FePt-C layer deposited on the MgO were investigated for the FePt-based heat assisted magnetic recording media. Stacking structure of the underlayer for the FePt-C layer was MgO (0-5 nm)/Cr80Mn20 (0-30 nm)/Cr50Ti50 (0-50 nm)/glass sub.. Surface observation result for the MgO film by using an atomic force microscope revealed the existence of nodules with a height of about 2 nm and a network-like convex structure with a height difference of about sub nm (boundary wall, BW) on the MgO crystal grain boundary. Density of the nodules largely depends on the surface roughness of the CrTi layer, RaCrTi and it is suppressed from 10 to 2/0.5 μm2 by reducing RaCrTi from 420 to 260 pm. Height of the BW depends on thickness of the MgO layer, tMgO and it can be suppressed by reducing tMgO to less than 4 nm. From the cross-sectional energy dispersive x-ray mapping, it is clarified that the BW is formed by atomic diffusion of Ti atoms from CrTi layer due to the substrate heating process, and a compound consists of Mg, Ti and O atoms. This BW can be used as a template to magnetically isolate the FePt column in the FePt-based granular film, such as FePt-SiO2, if the size of the BW is reduced to less than 10 nm. M-H loop of the FePt-C granular film deposited on the underlayer showed that the nodule and BW induce oxidation of the FePt grains, and reduction of intergranular exchange coupling.