First, you need an AIR SDK installed for signing an AIR application.
To make it convenient, make sure you’re on the environment variable PATH of the Adobe AIR SDK, i.e., /bin/ directory
Open a command prompt and go to the AIR application’s source folder (the source folder is the one that contains the applicaiton.xml file).
Note: Be sure that the Code Signing Certificate that you will use for signing is not in the source directory.
Run these Commands:
adt -package -storetype pkcs12 -keystore "c:\path\to\your\certificate.pfx" "c:\path\to\your\file.air" "application.xml"
Paths used as an Example:
For .pfx file: c:\path\to\your\certificate.pfx
For .air file: c:\path\to\your\file.air
If prompted enter the same password, you used while exporting the certificate as a .pfx file.
For more information read here.