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Recently, the demands for increasing memory capacities in hard disk drives (HDDs) has resulted in state-of-the-art technologies including heat assisted magnetic recording (HAMR) with significantly higher operating temperatures. HAMR results in swift degradation of current lubricant and carbon overcoat (COC) materials, leading to magnetic media corrosion which is detrimental to HDD operation. In addition, the lack of thorough understanding of the temperature profiles arising from the hotspot and energy management throughout these materials also exacerbates the problem. To address this issue, in this paper we will focus on the COC and investigate the transient heat transfer in various examples of nanoscale thin films when a hot spot is created via lattice Boltzmann method (LBM) since traditional conduction models like Fourier law are not accurate due to dominant sub-continuum effects. LBM originates from the Boltzmann transport equations (BTEs) and is computationally efficient due to easy parallelization with convenient handling of complex geometries. Our results of the heat transfer mechanism and temperature profiles show that Fourier equation under-predicts the peak temperature rise at the center of the hot-spot as the system size approaches the nanoscale domain. Applying LBM to a multilayered system, we observe a temperature slip along the interface of two materials indicated by the broken isothermal contours, as the heat is confined to a single layer. Using LBM, we then explore a novel graphene overcoat which has outstanding thermo-mechanical properties, and thereby extremely compatible in HAMR applications.