Common words:
* aerie (a nest of a bird of prey, especially an eagle, high up on a cliff or in a tree)
* aerial (relating to the air; existing or taking place in the air)
* aerobic (relating to, involving, or requiring free oxygen)
* aerosol (a substance packaged under pressure as a liquid, solid, or gas and released as a fine spray)
* aerodynamics (the study of the motion of air and other gases, and the forces acting on them)
* aeronaut (a person who navigates in an aircraft)
* aerostat (a lighter-than-air aircraft, such as a balloon or airship)
Less common words:
* aerobe (an organism that requires oxygen for growth)
* aerology (the science of the atmosphere)
* aerometer (an instrument for measuring the density of gases)
* aeronautics (the science or practice of designing, building, and operating aircraft)
* aeropause (the upper limit of the atmosphere)
* aerophone (a musical instrument that produces sound by vibrating a column of air)
* aerotaxis (the movement of an organism in response to a stimulus in the air)
Note: These words are mostly related to the air or flying. The "aer" prefix generally refers to the air or atmosphere.