The thermal properties of amorphous and crystalline phases in chalcogenide phase change materials (PCM) play a key role in device performance for non-volatile random-access memory. Here, we report the nanothermal morphology of amorphous and crystalline phases in laser pulsed GeTe and Ge2Sb2Te5 thin films by scanning thermal microscopy (SThM). By SThM measurements and quantitative finite element analysis simulations of two film thicknesses, the PCM thermal conductivities and thermal boundary conductances between the PCM and SThM probe are independently estimated for the amorphous and crystalline phase of each stoichiometry.