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I have been using MatterControl for a while now and although the layer fan is controllable from the "Controls" section of the program, once a print that should be using the fan begins, it never turns on. Which setting should enable the layer fan for different materials? I have tried min fan speed, max fan speed, and bridge fan speed and none seem to do what I want.

I do not use mattercontrol, but there is likely a checkbox that enables/disables the layer fan completely without altering the speeds. Look for this checkbox.