At committee stage, you can submit an amendment to delete an entire clause, but although it will be printed in the amendment paper, it will not be selected for debate. This is because each clause is already subject to a “clause stand part” debate, which gives you a chance to vote on whether it should remain part of the bill. So, if you want to leave out a clause you simply vote against the clause standing part of the bill.
At report stage, there are no clause stand part debates, so if you want to delete an entire clause, you need to submit an amendment to this effect.