Essentially, there is no way to erase a base. You can transfer all resources to other bases and sell off all defence and attack units which will lead to the base either being killed by the forgotten (on forgotten attack worlds) or by an enemy or random player who comes across the base and sees it is defenseless.
The base will still exist, however, in your base list and that will never go away. You may prefer just leaving the base as it is or convert it to a cash/tib/crystal generating base.