A novel combined setup, with a Scanning Thermal Microscope (SThM) embedded in a Scanning Electron Microscope (SEM), is used to characterize suspended nanotructures (nanowires and 2D materials) integrated in a microfabricated device. First, we analyze heat conduction within a rough silicon nanowire. The rough nature of the nanowire surface, which prohibits vacuum-SThM due to lose contact for heat dissipation, is circumvented by decorating the wire with periodic platinum dots. Reproducible approaches over these dots, enabled by the live feedback image provided by the SEM, yielded a strong improvement in thermal contact resistance and a higher accuracy in its estimation. The results – thermal resistance at the tip-sample contact of 188 ±3.7 K/W and equivalent axial thermal conductivity of the nanowire of 13.7 ±1.6 W/m·K – are obtained by performing a series of approach curves on the dots. Second, we study using vacuum-SThM heat conduction within a 2D material suspended between two microfabricated platforms that allows producing a thermal gradient in the nanomaterial. Thermal conductance and temperature along the nanomaterial are evaluated and compared with those obtained using Raman spectroscopy measurements. These works highlight the capabilities of the dual SThM/SEM instrument for investigating properties of nanostructures in highly controlled environments and its abilities, in particular the interest of systematic approach curves with well-positioned and monitored tip motion.