You can withdraw it as notes/coins or it can flow to non-bank accounts at ECB e.g. government. Usually these are not big numbers and what banks borrow from ECB is very close to what they keep at ECB (mininum reserve + deposits).
High level of deposit facility is a sign of a run on banks in countries with problems. Banks in such countries need to borrow money from ECB to be able to transfer client money to banks in safe countries. In this process safe banks accumulate "ECB money" in their current account at ECB. The safe banks then move the excess over their minimum reserve requirement to deposit account at ECB to get some interest.