This paper describes a new tool for eye-tracking data and their analysis with the use of interactive 3D models. This tool helps to analyse interactive 3D models easier than by time-consuming, frame-by-frame investigation of captured screen recordings with superimposed scanpaths. The main function of this tool, called 3DgazeR, is to calculate 3D coordinates (X, Y, Z coordinates of the 3D scene) for individual points of view. These 3D coordinates can be calculated from the values of the position and orientation of a virtual camera and the 2D coordinates of the gaze upon the screen. The functionality of 3DgazeR is introduced in a case study example using Digital Elevation Models as stimuli. The purpose of the case study was to verify the functionality of the tool and discover the most suitable visualization methods for geographic 3D models. Five selected methods are presented in the results section of the paper. Most of the output was created in a Geographic Information System. 3DgazeR works with generic CSV files, SMI eye-tracker, and the low-cost EyeTribe tracker connected with open source application OGAMA. It can compute 3D coordinates from raw data and fixations.