The engine capacity is:
(Vd - Vu) * Nc
Where Vd is the volume in the cylinder with the piston down, Vu is the volume with the cylinder up and Nc is the number of cylinders
The following volumes are cancelled out and are not included:
The volume that IS counted is the rest, usually called the swept volume (the volume the piston displaces when it sweeps).
That's why some people refer to 'capacity' as 'displacement'.
(see also Bore/Stroke ratios and Overbore Sizes and A-series engines for common capacities)