Empty the filter and reservoir, then rinse them both out with water. Put each part back in place.
Fill the water reservoir with a mixture of equal parts apple cider vinegar and warm water. Turn the percolator on and allow the vinegar and water to brew through the machine.
Turn off the percolator, allow it to cool, and then turn the appliance back on and run another mix of vinegar and water through a second brew cycle.
Wash the pot with hot, soapy water to remove any residue. Run two complete brew cycles with clean water to remove the vinegar from the percolator.