An important problem in processing the infrared detector material Hg1−xCdxTe is avoiding undue mercury loss. Here we quantify that loss and apply the information to the annealing of ion implanted Hg1−xCdxTe. We thus extend the work of Takitaetal. on Hg loss in HgTe to the ternary Hg1−xCdxTe. The Hg loss is generated with a thermal‐pulse annealing system and measured by Rutherford backscattering spectrometry (RBS). The loss rate is studied as a function of temperature, composition, and surface preparation (chemimechanical and contactless polishing). For each set of conditions the data is fit to an Arrhenius equationN⧠/t=A exp(−ΔE/kT) and the fitting parametersAand ΔEare determined. ΔEranges from 1.0 to 2.5 eV andAvaries from 1023to 1036atoms/cm2 s. Channeling RBS was also used to study the effect of thermal pulse annealing on boron implanted material. The rate of change of the minimum yield (χmin) with depth, which can be related to certain types of damage, was consistent with the calculated implant damage profile. A 260 °C 8 s anneal restored the crystal quality to better than the as‐received material, as observed by channeling.