Don't know about fragmenting, but an idea for merging could be allowing players to select multiple objects at once by holding down ctrl and providing a merge button.
Being able to select multiple tiles would also be useful if there's several things that one wants to change in the same way (say several characters of the game's font). You could just select them all and change them to char, cube or whatever in one go.
Edit: Actually for fragmenting there could be a fragment button that, when pressed while having something selected breaks it down to the individual tiles?
Just throwing around ideas, of course I don't know if any of this is actually doable within the system currently in place.