run cmd

then type ->  cd D:\Program Files\Adobe\Flex Builder 3 Plug-in\sdks\3.5\bin


Command :
adt -package -target native -storetype pkcs12 -keystore Personal Information Exchange output.exe input.air



where : Personal Information Exchange is an .p12 file which you can build when making and air file.

Example:
adt -package -target native -storetype pkcs12 -keystore C:\Workspace_Sharaku\SharakuPremium\Sharaku.p12 C:\Workspace_Sharaku\SharakuPremium\app.exe C:\Workspace_Sharaku\SharakuPremium\SharakuPremium.air