Free carrier absorption is a major component of the laser-induced breakdown of optical materials. Free carriers mediate intense absorption of incident laser light, and the resulting heat transfers to the lattice, generating more carriers, creating a catastrophic runaway process. Unfortunately, measurements at very low levels of free carriers relevant to laser breakdown are very difficult, particularly when measurements must be taken at highly elevated temperatures. This paper describes a photothermal common path interferometer (PCI) system that is enhanced by use of micromachined heaters to control local substrate temperatures. The temperature dependence of the free carrier absorption of aluminum oxide and silicon are measured. The aluminum oxide is shown to have essentially no variation in absorption with temperature up to 700K, but silicon shows an exponential increase as would be expected by the relative sizes of their bandgaps.