Van der Waals nanoscale structures are of great interest for both fundamental research and future technological applications, including heat dissipation in nano-electronic devices and thermoelectric applications. Therefore, characterization of the thermal properties of such structures are of great importance. The thermal transport in 2D materials depends strongly on the coupling to the underlying material and the temperature. Scanning Thermal Microscopy (SThM) is a leading technique for mapping thermal properties with nanoscale resolution , consisting of a self-heated probe which acts as a thermosensor during sample scanning. In this work, we report nanoscale thermal transport measurements at van der walls heterostructures formed by Molybdenum Disulphide (MoS2) and Graphene, as well as Franckeite which is natural heterostructure , by SThM in high vacuum. We demonstrate, for first time, that by cooling down the sample to temperatures as low as 150K and using doped Si probes, we are able to map the nanoscale heat transport in the heterostructures. We study the effect of the sample temperature on effective thermal conductivity of the heterostructures, by increasing the temperature up to 300K. In addition, for the franckeite we measure samples of different thicknesses and extract, for first time, the thermal conductivity of a single layer at various temperatures.