Eye-tracking based usability testing and User Experience (UX) research are widespread in the development processes of various types of software; however, there exist specific difficulties during usability tests of three-dimensional (3D) software. Analysing the screen records with gaze plots, heatmaps of fixations, and statistics of Areas of Interests (AOI), methodological problems occur when the participant wants to rotate, zoom, or move the 3D space. The data gained regarded the menu bar is mainly interpretable; however, the data regarded the 3D environment is hardly so, or not at all. Our research tested four software applications with the aforementioned problem in mind: ViveLab and Jack Digital Human Modelling (DHM) and ArchiCAD and CATIA Computer Aided Design (CAD) software. Our original goal was twofold. Firstly, with these usability tests, we aimed to identify issues in the software. Secondly, we tested the utility of a new methodology which was included in the tests. This paper summarizes the results on the methodology based on individual experiments with different software applications. One of the main ideas behind the methodology adopted is to tell the participants (during certain subtasks of the tests) not to move the 3D space while they perform the given tasks at a certain point in the usability test. During the experiments, we applied a Tobii eye-tracking device, and after the task completion, each participant was interviewed. Based on these experiences, the methodology appears to be both useful and applicable, and its visualisation techniques for one or more participants are interpretable.