Heat dissipation and thermal management are central challenges in various areas of science and technology and are critical issues for the majority of nanoelectronic devices. In this review, we focus on experimental advances in thermal characterization and phonon engineering that have drastically increased the understanding of heat transport and demonstrated efficient ways to control heat propagation in nanomaterials. We summarize the latest device-relevant methodologies of phonon engineering in semiconductor nanostructures and 2D materials, including graphene and transition metal dichalcogenides. Then, we review recent advances in thermal characterization techniques, and discuss their main challenges and limitations.