see upgrade guides and replica set index building guide as an overview of the task.

basically, take one secondary out of the set, start as a stand alone, perform operation, let it rejoin the set, and then repeat for other secondaries. When you get to the primary, do replSetStepDown, restart as a standalone, perform operation and then add it to the set.

caveats about not using rs.add()/rs.remove()

also mention using priorities to ensure that the right instance becomes primary after the operation.