If you want you could remove the overflow box put bulkheads in the holes and run a canister filter through them. You could have the intake be flush with the bottom of the tank so debris would just "drain" down into the canister filter and for the exit you could spray paint PCV black and have it run up to the surface for agitation using the other bulkhead. If your interested and have questions let me know.
Also to answer your original question. Yes you can probably pull out the overflow box but I agree with bob965 as far as just using bulkheads and capping them off. There's less of a chance of it leaking and it gives you more options in the future. (i.e. you want to sell the tank, you decide to use them)