This study aimed to develop a Thought Experiment Externalizer (TE-ext) and to apply it in order to observe barriers to problem solving. TE-ext enables students to visualize a problem situation. Users of TE-ext can implement changes in the situation and see the result as an animation. Experimental use of TE-ext identified three barriers to conducting an effective thought experiment (TE). First, participants tended not to change the situation from the original one; second, incorrect or inappropriate knowledge was applied to the situation; third, the participants did not apply the results of their TE to other situations. These factors prevented participants from rejecting their initial incorrect model and finding a new one through TEs.