The 3d edits are done by extracting the maps, models, props, and animations, into 3d software, extracting the replay data, and editing through the 3d software. This explanation is extremely oversimplified, but there's a youtube video called "Overview: How to make a CS:GO 3D-Edit like NikkyHD, Fuze or maro2k8!" by an0ther which overviews the process in more detail.