For example, you want to calculate cube file of MO(26)^2-MO(25)^2, boot up Multiwfn and input below commands
test.molden
200
3 // Export cube file containing orbital wavefunction
25,26 // The two orbitals needed later
2 // Medium quality grid
1 // Export grid data
Now you have orb000025.cub and orb000026.cub in current folder.

Reboot Multiwfn and input
orb000026.cub
13 // Process Grid data
11 // Grid data calculation
11 // A^2-B^2=C operation
orb000025.cub
Now, the grid data in memory corresponds to MO(26)^2-MO(25)^2, you can then use option -2 to visualize it, or use option 0 to export it as .cub file.