The objective of this paper is to obtain time-varying models of the thermal dynamics of a 3D hot thin film anemometer for Mars atmosphere. To this effect, a proof of concept prototype of the REMS (Rover Environmental Monitoring Station) wind sensor on board the Curiosity rover has been used. The self and cross-heating effects of the thermal structures have been characterized from open-loop measurements using Diffusive Representation. These models have been proven to be suitable in the analysis of the thermal dynamics of the sensor under constant temperature operation employing the tools of Sliding Mode Controllers. This analysis allows to understand the long term heat diffusion processes in the whole structure and how they may affect the raw output signals.