Frequency Domain Thermoreflectance (FDTR) is a versatile technique used to measure the thermal properties of thin films, multilayer stacks, and interfaces that govern the performance and thermal management in semiconductor microelectronics. Reliable thermal property measurements at these length scales (≈10 nm to ≈10 μm), where the physics of thermal transport and phonon scattering at interfaces both grow in complexity, are increasingly relevant as electronic components continue to shrink. While FDTR is a promising technique, FDTR instruments are generally home-built; they can be difficult to construct, align, and maintain, especially for the novice. Our goal here is to provide a practical resource beyond theory that increases the accessibility, replicability, and widespread adoption of FDTR instrumentation. We provide a detailed account of unpublished insights and institutional knowledge that are critical for obtaining accurate and repeatable measurements of thermal properties using FDTR. We discuss component selection and placement, alignment procedures, data collection parameters, common challenges, and our efforts to increase measurement automation. In FDTR, the unknown thermal properties are fit by minimizing the error between the phase lag at each frequency and the multilayer diffusive thermal model solution. For data fitting and uncertainty analysis, we compare common numerical integration methods, and we compare multiple approaches for fitting and uncertainty analysis, including Monte Carlo simulation, to demonstrate their reliability and relative speed. The instrument is validated with substrates of known thermal properties over a wide range of isotropic thermal conductivities, including Borofloat silica, quartz, sapphire, and silicon.