I am not asking which software to use to or how to remove atoms from a supercell. But rather how to decide which part should be removed. Like do I give preference to some surfaces or some particular molecules. Currently I am working with a layered material and that is why I am a bit confused. Like do I take the layer into the nano material or not and if I do take it then do I take one layer or two?
I am pretty sure that there exists some logical pointers that must be considered while cutting a structure. And things like make the structure more symmetric are also helpful. Any help is greatly appreciated.