Our Lady of Sorrows Hospital Parking Garage
Scully is walking to her car when she spies a message from Mulder written in the dust in episode 10x01 “My Struggle”.
Source: X-Files News
Secret Meeting Garage
Mulder is summoned to a meeting with a strange individual claiming that everyone's memory has been changed in episode 11x04 “The Lost Art of Forehead Sweat”.