What you mean by packing fraction in 3D?
Space occupied by particles/ Total volume of cell.
Packing fraction generally relates to the amount of space occupied inside a unit cell.
A unit cell can be of any dimension. We calculate the packing fraction appropriately.
If a unit cell is in 2-D, we use
Area occupied/Total area of unit cell
If a unit cell is in 3-D, we use
Volume occupied/Total volume of unit cell