This has been addressed in detail here:
There's just too much going on in the SS-D reports to accurately pull out ventilation loads alone. The post-processing approach may be your best bet, although it might be a bit cumbersome.
Alternately, you could try something like setting your ventilation load to zero and then subtracting the results from the model with mechanical ventilation. But you'll still want to do some post-processing, as there may be times where mechanical ventilation is helping certain zones and you don't want to take credit for it (basically acting like a partial economizer during certain hours even when you have your ventilation control method fixed).