When you bring up the mute menu in cbyt, it will take the header choice from old mute file. Unfortunately, the option is fixed as 2D shots for creating a new file. So you will have to enter NONE as old mute file name, then click Apply then End Picking. Close cbyt and edit the new mute file. There is a line
### offset, inline, crossline headers: 6 46 0
Those are headers for 2D shots. Change the 3 numbers to suit your needs:
Shot 3D 6 33 34
CMP 2D 6 7 0
CMP 3D 6 7 8
stack 2D 7 0 0
stack 3D 7 8 0
Then start cbyt, load your trace file and bring up mute menu and use the edited mute file