Temperature control in an RTP system can be improved by consideration of one or more witness structures different from the wafer (or other semiconductor object) being processed. For example, power coupling between the RTP heating system and witness structure can be used to adjust one or more control parameters, such as model definitions, that are used by the RTP system to control wafer heating. As another example, a stored trajectory of a desired witness structure temperature or other property can be used as a basis for control during a processing cycle. Thus, the witness structure may be controlled “closed-loop” while the wafer is heated “open-loop.” As a further example, a heat flux between the RTP heating system and witness structure can be used to determine radiant energy from the heating system that is incident on the witness structure. One or more control actions can be taken based on this incident energy.