In the analysis of thermal infrared data of asteroids by means of thermophysical models (TPMs) it is a common practice to neglect the uncertainty of the shape model and the rotational state, which are taken as an input for the model. Here, we present a novel method of investigating the importance of the shape model and the pole orientation uncertainties in the thermophysical modeling - the varied shape TPM (VS-TPM). Our method uses optical photometric data to generate various shape models that map the uncertainty in the shape and the rotational state. The TPM procedure is then run for all these shape models. We apply the implementation of the classical TPM as well as our VS-TPM to the convex shape models of several asteroids together with their thermal infrared data acquired by the NASA's Wide-field Infrared Survey Explorer (WISE) and compare the results. These show that the uncertainties of the shape model and the pole orientation can be very important (e.g., for the determination of the thermal inertia) and should be considered in the thermophysical analyses. We present thermophysical properties for six asteroids - (624) Hektor, (771) Libera, (1036) Ganymed, (1472) Muonio, (1627) Ivar, and (2606) Odessa.