You will need to do this for each runway that has ILS

1. Select the runway and press the Delete Key
2. This dialog will open warning you that this runway has a stock localizer (ILS) and that it cannot be removed permanently but can be orphaned.  It also reminds you to remove and approach code but we will deal with that later in any case
3. Click Yes.  The runway will be gone and the ILS will be orphaned north of the airport on the safe move limit for ILS.  It is important not to try and change this since if you do it might result in the original ILS appearing along with the orphaned one

Do not be tempted to use this method if you are changing the airport ICAO (for example if you don't have a ProKey).  You will end up with two ILS with the same identifier and that would not be a good thing.

IMPORTANT.  You will need a ProKey to complete this process.  If you do not have one then you can download a trial version.  Please also note that it you are changing an ICAO you will need the ProKey also to do that.  You will need version 1.66 or later to be able to edit the runway in the Raw Data View.  If you have an earlier version then please update.

Repeat this for each runway with an ILS

1. Select the runway and press Alt+Enter.  This opens the RDV dialog for the runway
2. The runway tree will be closed so click the little expand arrow to list everything
3. Select the ILS
4. Click the Delete Button
5. Close the RDV

The ILS feather should be deleted but you may find some left over bits like the Glide Slope.  This is just a drawing issue and is a result of using the direct access provided by the RDV.  You could save and reload the file to get rid of this but it really is not that important.  The ILS is gone.

Select each runway in turn and use the delete key to remove them.  If by chance you get the message about an ILS then go back to that step and deal with it

1. Go to the view menu and un-check Terrain Exclusions.  This is a very important step.  If you forget then the next step will remove your exclusion that gets rid of the airport background polygon.  NOTE that this applies to FSX and later.  For FS9 you should have created the bgl to remove the background in SBuilder so it will not be in the ADE project

Draw a rubber band around the whole airport.  This will select all the visible elements.  Use the  delete key to remove them. Finally use the View menu to re-show terrain exclusions.  You should now have an airport that looks a bit like this

• Now go the Lists and work through each list in turn.  If there is anything left over then delete it from the list.  
• Some lists:  Comms, Navaids and taxi designators will still have stuff in them.  In comms and navaids you will probably find some entries that can't be deleted.  These are informational.  In the screenshot above I am deleting the comms so I will select and delete those that I can (1) and leave the rest (2)

I found when I got to Scenery Objects that my rubber band was not set wide enough so I will delete these from the list

I probably don't need to delete taxi designators but I will to be sure that everything is gone.  Note that you can't remove the blank one

Don't get tempted to delete this terrain poly!  It the the exclusion rectangle that we have in place to remove the airport background polygon  (FSX and later only)

Switch to Approach Mode

In Approach Mode open List > Approaches and delete them.  You will need to do this one at a time since ADE currently does not allow multiple delete of approaches.

Now open the Navaid  and Way Point List in turn and delete as much as you can.

We can't remove the entry in the FS airport list but we can change the details so that it is clear that the airport is not in use.  Select Change Airport Reference Data from the Tools Menu

Change all the entries to 'Not in Use' or something similar which will remind you not to use this airport and click Change