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generally they're there to let the crankcase breathe, like with the PCV system.
Stupid question then...if I have a PCV valve can I just remove it and put a breather filter in there instead?
If you do that the suction effect is almost nill. The PCV valve pulls the crankcase fumes and pressures out. The inlet to complete the circuit is the breather on the other valve cover.
Usually, you can expect the PCV system to minimze crankcase pressures helping the rings to seal and reduce some power loss. Sometimes those pressures also cause or accelerate oil leaks past gaskets. Look at many race engines. They use a vacuum pump to get the job done.
You want some ventilation system.
Early system- There was a "breather" & a draft tube hanging down- worked when running (moving).
Positive Crankcase Ventilation uses breather & PCV valve. For emissions the breather was connected to the air filter.