How to create supercell in VESTA?

You may want to create supercell of a structure from CONTCAR file or any other file.

To do this, open the file in VESTA.

Go to Edit ---> Edit Data ---> Unit Cell.

Following dialogue box will appear. Click Transform.

In the below box, change the parameter in Rotation matrix and click OK.

Click OK for remaining dialogue boxes. You will get the super-cell in VESTA. You can save the output in different formats like .pdf, .xyz, .vesta, etc.

How to remove the atoms outside of the supercell or unitcell in VESTA?

During structure file generation for VASP calculation (POSCAR), you may see additional atoms outside of the unitcell or the supercell created. While this does not affect your calculation, for display, you would need atoms just inside the unit cell or supercell. This can be done by following way.

Open the file in VESTA
Go to Edit ---> Bonds
Select "Do not search atoms beyond the boundary"

This will solve your problem.