Probe systems and methods for automatically maintaining alignment between a probe and a device under test (DUT) during a temperature change. The methods include collecting an initial image of a planar offset fiducial and determining an initial height reference of a height offset fiducial. The methods further include changing a temperature of the DUT, automatically maintaining a planar alignment between a probe and the DUT during the changing, and automatically maintaining a height alignment between the probe and the BUT during the changing. The probe systems include a chuck, which defines a support surface configured to support a substrate that includes the DUT, and a probe head assembly, which includes a probe configured to contact a corresponding contact pad of the DUT. The probe systems further include a substrate thermal module, which is configured to regulate a temperature of the DUT, and a controller programmed to execute the methods.