Do I need to sanitize my air vents after I remove a bird from them?
There are a lot of diseases that vector from bird droppings.  The Illinois Department of Public Health mentions Histoplasmosis and Cryptococcus and several other diseases in HEALTH HAZARDS ASSOCIATED WITH BIRD AND BAT DROPPINGS.  They also recommend washing the area with soap and water if the area is small or contacting an environmental engineering consultant if the area is large.

NYC Health on their Pigeon-Related Diseases page recommends the following for large droppings:


  Large Amount of Droppings
  If you are planning a large clean-up of a structure, such as removing droppings from an air shaft, you should take protective measures to avoid health risks. Once the structure is cleaned, you should wash it regularly to prevent further accumulation of droppings.
  
  
  To minimize your risks for getting a pigeon-related disease, you should take the following precautions:
  Wear protective clothing, such as disposable coveralls, boots, and gloves. You can also wear a respirator to better protect yourself.
  If you are using a high-powered water hose to strip off dried droppings, be sure to control the dust. You can use plastic sheeting to contain the area, or you can wet down the work area. This will prevent inhalation, reduce the risk of infection and prevent dust from spreading outside the work area.
  You can avoid the risks of using a high-powered water hose by soaking the droppings in water and then shoveling them. Collect the wet material in heavy-duty plastic bags or other types of secure containers and discard it with the regular garbage.