Puede usar el comando "kill-pane".
kill-pane [-a] [-t target-pane]
(alias: killp)
Destroy the given pane. If no panes remain in the containing window, it is also destroyed. The -a option kills all but the pane given with -t.
Entonces, por ejemplo, si desea eliminar todos los paneles, excepto el panel 0:
kill-pane -a -t 0
Si no sabe cuáles son sus números de panel, puede usar el comando "paneles de visualización":
display-panes [-t target-client]
(alias: displayp)
Display a visible indicator of each pane shown by target-client. See the display-panes-time, display-panes-colour, and display-panes-active-colour
session options. While the indicator is on screen, a pane may be selected with the '0' to '9' keys.