I assume a module cutter here, but the same rules would apply to any modular ship.
Could treat it as a 20 ton ship (with docking clamps, and drives/power plant appropriate for a 50 ton ship). The modules would be priced as a 30 ton ship with the appropriate costs for whatever you put in it. Obviously, you wouldn't need maneuver drives, powerplants, or computers for that 30 ton module - those are already in the remaining 20 ton ship part.
Or, it is a 50 ton ship with a 30 ton "bay", which is essentially an empty 30 ton removable cargo bay module. Additional modules would be created as a 30 ton ship (again, without drives as those are already in the rest of the ship). Similar to a 50 ton weapon bay - built into the ship, but the bay can be removed and replaced with another bay weapon easily. (This is the way the cutter would work in my games.)
I guess basically I'm saying, either way you look at a modular ship, design the modules as you would a ship - just leave out the parts you don't need like drives and such. So as Andrew said - the price of the hull + the components you want.